A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process

[1]  E. Birney,et al.  Pfam: the protein families database , 2013, Nucleic Acids Res..

[2]  Jürgen Kurths,et al.  Recurrence plots for the analysis of complex systems , 2009 .

[3]  Y. Ishino,et al.  Mechanism of replication machinery assembly as revealed by the DNA ligase–PCNA–DNA complex architecture , 2009, Proceedings of the National Academy of Sciences.

[4]  G. Böhm,et al.  Relevance of sequence statistics for the properties of extremophilic proteins. , 2009, International journal of peptide and protein research.

[5]  T. Yasunaga,et al.  Detection of circulating Asian H5N1 viruses by a newly established monoclonal antibody. , 2009, Biochemical and biophysical research communications.

[6]  A. Godzik,et al.  Comparison of sequence profiles. Strategies for structural predictions using sequence information , 2008, Protein science : a publication of the Protein Society.

[7]  P. Tien,et al.  Analysis of a point mutation in H5N1 avian influenza virus hemagglutinin in relation to virus entry into live mammalian cells , 2008, Archives of Virology.

[8]  P. Balaram.  De novo design: backbone conformational constraints in nucleating helices and beta-hairpins. , 2008, The journal of peptide research : official journal of the American Peptide Society.

[9]  A. J. Perez-Berna,et al.  The pre-transmembrane region of the HCV E1 envelope glycoprotein: interaction with model membranes. , 2008, Biochimica et biophysica acta.

[10]  Janusz M. Bujnicki,et al.  MetaMQAP: A meta-server for the quality assessment of protein models , 2008, BMC Bioinformatics.

[11]  Collin M. Stultz,et al.  The Effect of a ΔK280 Mutation on the Unfolded State of a Microtubule-Binding Repeat in Tau , 2008, PLoS Comput. Biol..

[12]  N. Veljkovic,et al.  AIDS vaccine: efficacy, safety and ethics. , 2008, Vaccine.

[13]  Burak Erman,et al.  Prediction of binding sites in receptor-ligand complexes with the Gaussian Network Model. , 2008, Physical review letters.

[14]  Kuo-Bin Li,et al.  Remote protein homology detection using recurrence quantification analysis and amino acid physicochemical properties. , 2008, Journal of theoretical biology.

[15]  N. Veljkovic,et al.  EMILINs interact with anthrax protective antigen and inhibit toxin action in vitro. , 2008, Matrix biology : journal of the International Society for Matrix Biology.

[16]  N. Veljkovic,et al.  Lipoprotein lipase: A bioinformatics criterion for assessment of mutations as a risk factor for cardiovascular disease , 2008, Proteins.

[17]  D. Chang,et al.  Membrane interaction and structure of the transmembrane domain of influenza hemagglutinin and its fusion peptide complex. , 2008 .

[18]  N. Zanchin,et al.  The Shwachman-Bodian-Diamond syndrome associated protein interacts with HsNip7 and its down-regulation affects gene expression at the transcriptional and translational levels. , 2007, Experimental cell research.

[19]  Fei Long,et al.  BALBES: a molecular-replacement pipeline , 2007, Acta crystallographica. Section D, Biological crystallography.

[20]  Jianguo Wu,et al.  Origin of highly pathogenic H5N1 avian influenza virus in China and genetic characterization of donor and recipient viruses. , 2007, The Journal of general virology.

[21]  S. Emerson,et al.  Isolation and Characterization of Broadly Neutralizing Human Monoclonal Antibodies to the E1 Glycoprotein of Hepatitis C Virus , 2007, Journal of Virology.

[22]  R. Peralta,et al.  Probing the role of the divalent metal ion in uteroferrin using metal ion replacement and a comparison to isostructural biomimetics , 2007, JBIC Journal of Biological Inorganic Chemistry.

[23]  Michal Boniecki,et al.  Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms2io6A37 in tRNA , 2007, Proteins.

[24]  K. Henrick,et al.  Inference of macromolecular assemblies from crystalline state. , 2007, Journal of molecular biology.

[25]  Akiko Shimamura,et al.  The human Shwachman-Diamond syndrome protein, SBDS, associates with ribosomal RNA. , 2007, Blood.

[26]  R. Goldstein.  Amino‐acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: Insights from the quasi‐chemical approximation , 2007, Protein science : a publication of the Protein Society.

[27]  Michail Yu. Lobanov,et al.  Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms , 2007, Bioinform..

[28]  L. Gahan,et al.  The reaction mechanism of the Ga(III)Zn(II) derivative of uteroferrin and corresponding biomimetics , 2007, JBIC Journal of Biological Inorganic Chemistry.

[29]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[30]  William N. Hunter,et al.  The Non-mevalonate Pathway of Isoprenoid Precursor Biosynthesis* , 2007, Journal of Biological Chemistry.

[31]  A. Hengge,et al.  Diesterase activity and substrate binding in purple acid phosphatases. , 2007, Journal of the American Chemical Society.

[32]  Marcin Feder,et al.  Type II restriction endonuclease R.Eco29kI is a member of the GIY-YIG nuclease superfamily , 2007, BMC Structural Biology.

[33]  Jens Carlsson,et al.  Structures of Mycobacterium tuberculosis 1-Deoxy-D-xylulose-5-phosphate Reductoisomerase Provide New Insights into Catalysis* , 2007, Journal of Biological Chemistry.

[34]  Janusz M Bujnicki,et al.  A model of restriction endonuclease MvaI in complex with DNA: A template for interpretation of experimental data and a guide for specificity engineering , 2007, Proteins.

[35]  J. Bujnicki,et al.  Identification of a single HNH active site in type IIS restriction endonuclease Eco31I. , 2007, Journal of molecular biology.

[36]  A. Giuliani,et al.  Simulated Point Mutations in the Aα-Chain of Human Fibrinogen Support a Role of the αC Domain in the Stabilization of Fibrin Gel , 2007, Pathophysiology of Haemostasis and Thrombosis.

[37]  F. Penin,et al.  Characterization of Fusion Determinants Points to the Involvement of Three Discrete Regions of Both E1 and E2 Glycoproteins in the Membrane Fusion Process of Hepatitis C Virus , 2007, Journal of Virology.

[38]  R. Peralta,et al.  An unprecedented Fe(III)(mu-OH)Zn(II) complex that mimics the structural and functional properties of purple acid phosphatases. , 2007, Journal of the American Chemical Society.

[39]  H. Drummer,et al.  Mutagenesis of a conserved fusion peptide-like motif and membrane-proximal heptad-repeat region of hepatitis C virus glycoprotein E1. , 2007, The Journal of general virology.

[40]  R. Greaves,et al.  Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles , 2007, BMC Structural Biology.

[41]  V. Hilser,et al.  Functional residues serve a dominant role in mediating the cooperativity of the protein ensemble , 2007, Proceedings of the National Academy of Sciences.

[42]  Michael Costanzo,et al.  The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast , 2007, Nature Genetics.

[43]  Benjamin J. Raphael,et al.  The Sorcerer II Global Ocean Sampling Expedition: Expanding the Universe of Protein Families , 2007, PLoS biology.

[44]  J. Bujnicki,et al.  Novel protein fold discovered in the PabI family of restriction enzymes , 2007, Nucleic acids research.

[45]  Homme W Hellinga,et al.  Protein fabrication automation , 2007, Protein science : a publication of the Protein Society.

[46]  H. Morii,et al.  Biosynthesis of Ether-Type Polar Lipids in Archaea and Evolutionary Considerations , 2007, Microbiology and Molecular Biology Reviews.

[47]  V. Šikšnys,et al.  Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically , 2007, Nucleic acids research.

[48]  Philip E. Bourne,et al.  Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2 , 2007, BMC Bioinformatics.

[49]  U. Dietrich,et al.  Application of the EIIP/ISM bioinformatics concept in development of new drugs. , 2007, Current medicinal chemistry.

[50]  F. Penin,et al.  Transmembrane Domains of Hepatitis C Virus Envelope Glycoproteins: Residues Involved in E1E2 Heterodimerization and Involvement of These Domains in Virus Entry , 2006, Journal of Virology.

[51]  Michelle G. Giglio,et al.  TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes , 2006, Nucleic Acids Res..

[52]  Stephen D. Bell,et al.  DNA Replication in the Archaea , 2006, Microbiology and Molecular Biology Reviews.

[53]  K. Resing,et al.  The gatekeeper residue controls autoactivation of ERK2 via a pathway of intramolecular connectivity , 2006, Proceedings of the National Academy of Sciences.

[54]  L. Maródi,et al.  Severe Shwachman-Diamond syndrome phenotype caused by compound heterozygous missense mutations in the SBDS gene. , 2006, Experimental hematology.

[55]  M. Ellingham,et al.  Selection and characterization of RNA aptamers to the RNA-dependent RNA polymerase from foot-and-mouth disease virus. , 2006, RNA.

[56]  Xiaoliang Liang,et al.  The roles of surface loop insertions and disulfide bond in the stabilization of thermophilic WF146 protease , 2006, FEBS letters.

[57]  B. Bassler,et al.  Ligand-Induced Asymmetry in Histidine Sensor Kinase Complex Regulates Quorum Sensing , 2006, Cell.

[58]  H. Hellinga,et al.  The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites. , 2006, Journal of molecular biology.

[59]  Andrew G. Watts,et al.  Conservation of Structure and Mechanism in Primary and Secondary Transporters Exemplified by SiaP, a Sialic Acid Binding Virulence Factor from Haemophilus influenzae* , 2006, Journal of Biological Chemistry.

[60]  D. Hume,et al.  Identification and molecular modeling of a novel, plant-like, human purple acid phosphatase. , 2006, Gene.

[61]  J. Wiesner,et al.  Fosmidomycin plus Clindamycin for Treatment of Pediatric Patients Aged 1 to 14 Years with Plasmodium falciparum Malaria , 2006, Antimicrobial Agents and Chemotherapy.

[62]  E. Blanchard,et al.  Hepatitis C Virus Entry Depends on Clathrin-Mediated Endocytosis , 2006, Journal of Virology.

[63]  Gabrielle A. Reeves,et al.  Structural diversity of domain superfamilies in the CATH database. , 2006, Journal of molecular biology.

[64]  David Tollervey,et al.  RNA-quality control by the exosome , 2006, Nature Reviews Molecular Cell Biology.

[65]  H. Kanegane,et al.  Clinical and genetic analyses of presumed shwachman-diamond syndrome in Japan , 2006, International journal of hematology.

[66]  Liangjiang Wang,et al.  BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences , 2006, Nucleic Acids Res..

[67]  Seungwoo Hwang,et al.  Using evolutionary and structural information to predict DNA‐binding sites on DNA‐binding proteins , 2006, Proteins.

[68]  J. M. Scholtz,et al.  Lessons in stability from thermophilic proteins , 2006, Protein science : a publication of the Protein Society.

[69]  D. O’Leary,et al.  Secondary structure spatial conformation footprint: a novel method for fast protein structure comparison and classification , 2006, BMC Structural Biology.

[70]  R. Bahadur,et al.  ProFace: a server for the analysis of the physicochemical features of protein-protein interfaces , 2006, BMC Structural Biology.

[71]  J. Rommens,et al.  Phylogeny, sequence conservation, and functional complementation of the SBDS protein family. , 2006, Genomics.

[72]  L. Guddat,et al.  The catalytic mechanisms of binuclear metallohydrolases. , 2006, Chemical reviews.

[73]  Vasant Honavar,et al.  Predicting DNA-binding sites of proteins from amino acid sequence , 2006, BMC Bioinformatics.

[74]  B. Patel,et al.  Crystal structure of AmyA lacks acidic surface and provide insights into protein stability at poly‐extreme condition , 2006, FEBS letters.

[75]  C. Voisset,et al.  Hepatitis C virus entry: potential receptors and their biological functions. , 2006, The Journal of general virology.

[76]  Tom L Blundell,et al.  An algorithm for predicting protein–protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements , 2006, Protein science : a publication of the Protein Society.

[77]  D. Pignol,et al.  Genetic and Biochemical Evidence for the Involvement of a Molybdenum-Dependent Enzyme in One of the Selenite Reduction Pathways of Rhodobacter sphaeroides f. sp. denitrificans IL106 , 2006, Applied and Environmental Microbiology.

[78]  Marcin Feder,et al.  Phylogenomic analysis of the GIY-YIG nuclease superfamily , 2006, BMC Genomics.

[79]  Jean-François Gibrat,et al.  ROC and confusion analysis of structure comparison methods identify the main causes of divergence from manual protein classification , 2006, BMC Bioinform..

[80]  Vojtech Spiwok,et al.  Modelling of carbohydrate–aromatic interactions: ab initio energetics and force field performance , 2006, J. Comput. Aided Mol. Des..

[81]  Nick V Grishin,et al.  A tale of two ferredoxins: sequence similarity and structural differences , 2006 .

[82]  R. Mariuzza.  Multiple paths to multispecificity. , 2006, Immunity.

[83]  F. Spener,et al.  Recombinant purple acid phosphatase isoform 3 from sweet potato is an enzyme with a diiron metal center , 2006, The FEBS journal.

[84]  Shandar Ahmad,et al.  Dimensionality of amino acid space and solvent accessibility prediction with neural networks , 2006, Comput. Biol. Chem..

[85]  Dinakar M Salunke,et al.  Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response. , 2006, Immunity.

[86]  Sean R. Collins,et al.  Global landscape of protein complexes in the yeast Saccharomyces cerevisiae , 2006, Nature.

[87]  K. Britton,et al.  Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[88]  J. Soppa.  From genomes to function: haloarchaea as model organisms. , 2006, Microbiology.

[89]  A. J. Perez-Berna,et al.  The membrane-active regions of the hepatitis C virus E1 and E2 envelope glycoproteins. , 2006, Biochemistry.

[90]  F. Penin,et al.  Hepatitis C Virus Glycoproteins Mediate Low pH-dependent Membrane Fusion with Liposomes* , 2006, Journal of Biological Chemistry.

[91]  Y. Iwasa,et al.  Genetic Addiction: Selfish Gene's Strategy for Symbiosis in the Genome , 2006, Genetics.

[92]  R. Hohl,et al.  Anti-cancer therapy: targeting the mevalonate pathway. , 2006, Current cancer drug targets.

[93]  Milton H. Saier,et al.  TCDB: the Transporter Classification Database for membrane transport protein analyses and information , 2005, Nucleic Acids Res..

[94]  I. Bahar,et al.  Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[95]  D. Pignol,et al.  A papain-like enzyme at work: native and acyl-enzyme intermediate structures in phytochelatin synthesis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[96]  H. Viadiu,et al.  A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA , 2005, The EMBO journal.

[97]  A. Bracher,et al.  Structure of a halophilic nucleoside diphosphate kinase from Halobacterium salinarum , 2005, FEBS letters.

[98]  M. Gerstein,et al.  Global analysis of protein phosphorylation in yeast , 2005, Nature.

[99]  Arne Elofsson,et al.  Pcons5: combining consensus, structural evaluation and fold recognition scores , 2005, Bioinform..

[100]  Alessandra Corazza,et al.  Structure, conformational stability, and enzymatic properties of acylphosphatase from the hyperthermophile Sulfolobus solfataricus , 2005, Proteins.

[101]  L. Kay,et al.  Intrinsic dynamics of an enzyme underlies catalysis , 2005, Nature.

[102]  Robert Huber,et al.  Structure of the metal-independent restriction enzyme BfiI reveals fusion of a specific DNA-binding domain with a nonspecific nuclease. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[103]  Gaynor A Randle,et al.  Sialic acid transport in Haemophilus influenzae is essential for lipopolysaccharide sialylation and serum resistance and is dependent on a novel tripartite ATP‐independent periplasmic transporter , 2005, Molecular microbiology.

[104]  Barry Honig,et al.  Retroviral matrix domains share electrostatic homology: models for membrane binding function throughout the viral life cycle. , 2005, Structure.

[105]  Eugene I Shakhnovich,et al.  Physics and evolution of thermophilic adaptation. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[106]  Charles M. Rice,et al.  Unravelling hepatitis C virus replication from genome to function , 2005, Nature.

[107]  R. Leary,et al.  The Shwachman-Diamond SBDS protein localizes to the nucleolus. , 2005, Blood.

[108]  T. D. de Jongh,et al.  Direct observation of multiple protonation states in recombinant human purple acid phosphatase , 2005, JBIC Journal of Biological Inorganic Chemistry.

[109]  Edita Kriukienė,et al.  MnlI--The member of H-N-H subtype of Type IIS restriction endonucleases. , 2005, Biochimica et biophysica acta.

[110]  N. Sträter,et al.  Crystal structures of recombinant human purple Acid phosphatase with and without an inhibitory conformation of the repression loop. , 2005, Journal of molecular biology.

[111]  Sándor Pongor,et al.  Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm , 2005, Bioinform..

[112]  Adam Godzik,et al.  Connecting the protein structure universe by using sparse recurring fragments. , 2005, Structure.

[113]  B. Kawakami,et al.  Discovery of a novel restriction endonuclease by genome comparison and application of a wheat-germ-based cell-free translation assay: PabI (5′-GTA/C) from the hyperthermophilic archaeon Pyrococcus abyssi , 2005, Nucleic acids research.

[114]  Marcin Feder,et al.  The PD-(D/E)XK superfamily revisited: identification of new members among proteins involved in DNA metabolism and functional predictions for domains of (hitherto) unknown function , 2005, BMC Bioinformatics.

[115]  Itay Mayrose,et al.  ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures , 2005, Nucleic Acids Res..

[116]  Johannes Söding,et al.  The HHpred interactive server for protein homology detection and structure prediction , 2005, Nucleic Acids Res..

[117]  Leszek Rychlewski,et al.  FFAS03: a server for profile–profile sequence alignments , 2005, Nucleic Acids Res..

[118]  P. Weers,et al.  Role of buried polar residues in helix bundle stability and lipid binding of apolipophorin III: destabilization by threonine 31. , 2005, Biochemistry.

[119]  B. Ranjbar,et al.  Deglycosylation of glucoamylase from Aspergillus niger: effects on structure, activity and stability. , 2005, Biochimica et biophysica acta.

[120]  John Moult,et al.  A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. , 2005, Current opinion in structural biology.

[121]  Russell L. Marsden,et al.  Progress of structural genomics initiatives: an analysis of solved target structures. , 2005, Journal of molecular biology.

[122]  J. Rommens,et al.  Structural and Mutational Analysis of the SBDS Protein Family , 2005, Journal of Biological Chemistry.

[123]  T. Hughes,et al.  The Shwachman-Bodian-Diamond Syndrome Protein Family Is Involved in RNA Metabolism* , 2005, Journal of Biological Chemistry.

[124]  Joost Schymkowitz,et al.  Recognizing and defining true Ras binding domains II: in silico prediction based on homology modelling and energy calculations. , 2005, Journal of molecular biology.

[125]  Arne Elofsson,et al.  All are not equal: A benchmark of different homology modeling programs , 2005, Protein science : a publication of the Protein Society.

[126]  B. Assael,et al.  Identification of novel mutations in patients with Shwachman‐Diamond syndrome , 2005, Human mutation.

[127]  Mohd Firdaus Raih,et al.  Solvent accessibility in native and isolated domain environments: general features and implications to interface predictability. , 2005, Biophysical chemistry.

[128]  J. Bujnicki,et al.  A theoretical model of restriction endonuclease NlaIV in complex with DNA, predicted by fold recognition and validated by site-directed mutagenesis and circular dichroism spectroscopy. , 2005, Protein engineering, design & selection : PEDS.

[129]  Ming-Tat Ko,et al.  Amino acid coupling patterns in thermophilic proteins , 2005, Proteins.

[130]  Johannes Söding,et al.  Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..

[131]  B. Van Houten,et al.  Structural insights into the first incision reaction during nucleotide excision repair , 2005, The EMBO journal.

[132]  A Pandini,et al.  Conservation and specialization in PAS domain dynamics. , 2005, Protein engineering, design & selection : PEDS.

[133]  A. Pingoud,et al.  Type II restriction endonucleases: structure and mechanism , 2005, Cellular and Molecular Life Sciences.

[134]  Shandar Ahmad,et al.  PSSM-based prediction of DNA binding sites in proteins , 2005, BMC Bioinformatics.

[135]  Marcin Feder,et al.  Identification of a new family of putative PD-(D/E)XK nucleases with unusual phylogenomic distribution and a new type of the active site , 2005, BMC Genomics.

[136]  J. Bujnicki,et al.  Specificity Changes in the Evolution of Type II Restriction Endonucleases , 2005, Journal of Biological Chemistry.

[137]  Su-Ying Wu,et al.  Structural and biochemical studies of human proliferating cell nuclear antigen complexes provide a rationale for cyclin association and inhibitor design. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[138]  Ozlem Keskin,et al.  Protein Interactions and Fluctuations in a Proteomic Network using an Elastic Network Model , 2005, Journal of biomolecular structure & dynamics.

[139]  S. Brunak,et al.  Prediction, conservation analysis, and structural characterization of mammalian mucin-type O-glycosylation sites. , 2005, Glycobiology.

[140]  J. Bujnicki,et al.  Interaction preferences across protein-protein interfaces of obligatory and non-obligatory components are different , 2005, BMC Structural Biology.

[141]  K. Katoh,et al.  MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.

[142]  Lei Wang,et al.  Accuracy of structure-derived properties in simple comparative models of protein structures , 2005, Nucleic acids research.

[143]  L. Guddat,et al.  Phosphate forms an unusual tripodal complex with the Fe-Mn center of sweet potato purple acid phosphatase. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[144]  B. Somogyi,et al.  A simple model for the cooperative stabilisation of actin filaments by phalloidin and jasplakinolide , 2005, FEBS letters.

[145]  Leszek Rychlewski,et al.  LiveBench‐8: The large‐scale, continuous assessment of automated protein structure prediction , 2005, Protein science : a publication of the Protein Society.

[146]  Liisa Holm,et al.  ADDA: a domain database with global coverage of the protein universe , 2004, Nucleic Acids Res..

[147]  Cathy H. Wu,et al.  InterPro, progress and status in 2005 , 2004, Nucleic Acids Res..

[148]  W. Eisenreich,et al.  Hexameric Assembly of the Bifunctional Methylerythritol 2,4-Cyclodiphosphate Synthase and Protein-Protein Associations in the Deoxy-xylulose-dependent Pathway of Isoprenoid Precursor Biosynthesis* , 2004, Journal of Biological Chemistry.

[149]  R. MacKinnon,et al.  Glycine as a D-amino acid surrogate in the K(+)-selectivity filter. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[150]  R. Wilson,et al.  Mutations of the SBDS gene are present in most patients with Shwachman-Diamond syndrome. , 2004, Blood.

[151]  K Henrick,et al.  Electronic Reprint Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions Biological Crystallography Secondary-structure Matching (ssm), a New Tool for Fast Protein Structure Alignment in Three Dimensions , 2022 .

[152]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[153]  Jie Liang,et al.  Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. , 2004, Journal of molecular biology.

[154]  P J Winn,et al.  Issues in high‐throughput comparative modelling: A case study using the ubiquitin E2 conjugating enzymes , 2004, Proteins.

[155]  D. Schneider.  Rendezvous in a membrane: close packing, hydrogen bonding, and the formation of transmembrane helix oligomers , 2004, FEBS letters.

[156]  D. Bussiere,et al.  Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase from Shewanella oneidensis at 1.6 A: identification of farnesyl pyrophosphate trapped in a hydrophobic cavity. , 2004, Acta crystallographica. Section D, Biological crystallography.

[157]  David Baker,et al.  Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[158]  C. Rice,et al.  An N-Terminal Amphipathic Helix in Hepatitis C Virus (HCV) NS4B Mediates Membrane Association, Correct Localization of Replication Complex Proteins, and HCV RNA Replication , 2004, Journal of Virology.

[159]  K. Linton,et al.  The ATP switch model for ABC transporters , 2004, Nature Structural &Molecular Biology.

[160]  Conrad C. Huang,et al.  UCSF Chimera—A visualization system for exploratory research and analysis , 2004, J. Comput. Chem..

[161]  Shigeyuki Yokoyama,et al.  Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8 , 2004, Journal of Structural and Functional Genomics.

[162]  Aleksey Porollo,et al.  PROTEINS: Structure, Function, and Bioinformatics 56:753–767 (2004) Accurate Prediction of Solvent Accessibility Using Neural Networks–Based Regression , 2022 .

[163]  Iosif I Vaisman,et al.  A simple topological representation of protein structure: Implications for new, fast, and robust structural classification , 2004, Proteins.

[164]  Alessandro Senes,et al.  Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs. , 2004, Current opinion in structural biology.

[165]  Roberto Sanchez,et al.  Systematic analysis of added-value in simple comparative models of protein structure. , 2004, Structure.

[166]  G. Wilson,et al.  Direct electrochemistry of porcine purple acid phosphatase (uteroferrin). , 2004, Biochemistry.

[167]  H. Drummer,et al.  Hepatitis C Virus Glycoprotein E2 Contains a Membrane-proximal Heptad Repeat Sequence That Is Essential for E1E2 Glycoprotein Heterodimerization and Viral Entry* , 2004, Journal of Biological Chemistry.

[168]  Jean-Michel Claverie,et al.  CaspR: a web server for automated molecular replacement using homology modelling , 2004, Nucleic Acids Res..

[169]  Janusz M. Bujnicki,et al.  COLORADO3D, a web server for the visual analysis of protein structures , 2004, Nucleic Acids Res..

[170]  Karsten Suhre,et al.  ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement , 2004, Nucleic Acids Res..

[171]  J. Boucher,et al.  Inhibitor coordination interactions in the binuclear manganese cluster of arginase. , 2004, Biochemistry.

[172]  Jue Chen,et al.  ATP-binding cassette transporters in bacteria. , 2004, Annual review of biochemistry.

[173]  Stella Veretnik,et al.  Toward consistent assignment of structural domains in proteins. , 2004, Journal of molecular biology.

[174]  Hongyi Zhou,et al.  Single‐body residue‐level knowledge‐based energy score combined with sequence‐profile and secondary structure information for fold recognition , 2004, Proteins.

[175]  S. Halford,et al.  Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA. , 2004, Journal of molecular biology.

[176]  Shaomin Yan,et al.  Fate of 130 hemagglutinins from different influenza A viruses. , 2004, Biochemical and biophysical research communications.

[177]  B. Somogyi,et al.  The effect of phalloidin and jasplakinolide on the flexibility and thermal stability of actin filaments , 2004, FEBS letters.

[178]  Shandar Ahmad,et al.  ASAView: Database and tool for solvent accessibility representation in proteins , 2003, BMC Bioinformatics.

[179]  D. Hume,et al.  Phosphotyrosyl peptides and analogues as substrates and inhibitors of purple acid phosphatases. , 2004, Archives of biochemistry and biophysics.

[180]  A. Sali,et al.  Alignment of protein sequences by their profiles , 2004, Protein science : a publication of the Protein Society.

[181]  Petety V Balaji,et al.  Identification of common structural features of binding sites in galactose‐specific proteins , 2004, Proteins.

[182]  Sung-Hou Kim,et al.  Local feature frequency profile: a method to measure structural similarity in proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[183]  M. Vieth,et al.  Kinomics-structural biology and chemogenomics of kinase inhibitors and targets. , 2004, Biochimica et biophysica acta.

[184]  Virander S. Chauhan,et al.  De novo design and characterization of a helical hairpin eicosapeptide; emergence of an anion receptor in the linker region. , 2004, Structure.

[185]  Shandar Ahmad,et al.  Analysis and prediction of DNA-binding proteins and their binding residues based on composition, sequence and structural information , 2004, Bioinform..

[186]  Robert C. Edgar,et al.  MUSCLE: multiple sequence alignment with high accuracy and high throughput. , 2004, Nucleic acids research.

[187]  K. Stiasny,et al.  Structure of a flavivirus envelope glycoprotein in its low‐pH‐induced membrane fusion conformation , 2004, The EMBO journal.

[188]  Kay Diederichs,et al.  Cation-π Interactions as Determinants for Binding of the Compatible Solutes Glycine Betaine and Proline Betaine by the Periplasmic Ligand-binding Protein ProX from Escherichia coli* , 2004, Journal of Biological Chemistry.

[189]  Y. Makita,et al.  Novel SBDS mutations caused by gene conversion in Japanese patients with Shwachman-Diamond syndrome , 2004, Human Genetics.

[190]  Y. Modis,et al.  Structure of the dengue virus envelope protein after membrane fusion , 2004, Nature.

[191]  J. Lepault,et al.  Conformational change and protein–protein interactions of the fusion protein of Semliki Forest virus , 2004, Nature.

[192]  J. Tainer,et al.  Structural Basis for FEN-1 Substrate Specificity and PCNA-Mediated Activation in DNA Replication and Repair , 2004, Cell.

[193]  D. Krüger,et al.  Crystal structure of type IIE restriction endonuclease EcoRII reveals an autoinhibition mechanism by a novel effector-binding fold. , 2004, Journal of molecular biology.

[194]  N. Veljkovic,et al.  MOLECULAR MAKEUP OF HIV-1 ENVELOPE PROTEIN , 2004, International reviews of immunology.

[195]  Hao Fan,et al.  Refinement of homology‐based protein structures by molecular dynamics simulation techniques , 2004, Protein science : a publication of the Protein Society.

[196]  J. Badia,et al.  Functional characterization of the Escherichia coli K-12 yiaMNO transport protein genes , 2004, Molecular membrane biology.

[197]  Laurence H Pearl,et al.  Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the β‐clamp , 2003, The EMBO journal.

[198]  Andrzej Kolinski,et al.  Protein fragment reconstruction using various modeling techniques , 2003, J. Comput. Aided Mol. Des..

[199]  E. O’Shea,et al.  Global analysis of protein localization in budding yeast , 2003, Nature.

[200]  D. Baker,et al.  Coupled prediction of protein secondary and tertiary structure , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[201]  Dan S. Tawfik,et al.  The specificity of cross‐reactivity: Promiscuous antibody binding involves specific hydrogen bonds rather than nonspecific hydrophobic stickiness , 2003, Protein science : a publication of the Protein Society.

[202]  Janusz M Bujnicki,et al.  Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology. , 2003, Current protein & peptide science.

[203]  Darren A. Natale,et al.  The COG database: an updated version includes eukaryotes , 2003, BMC Bioinformatics.

[204]  A. Godzik,et al.  Homology modeling provides insights into the binding mode of the PAAD/DAPIN/pyrin domain, a fourth member of the CARD/DD/DED domain family , 2003, Protein science : a publication of the Protein Society.

[205]  Shandar Ahmad,et al.  Design and training of a neural network for predicting the solvent accessibility of proteins , 2003, J. Comput. Chem..

[206]  T. Poulos,et al.  New understandings of thermostable and peizostable enzymes. , 2003, Current opinion in biotechnology.

[207]  G. Phillips,et al.  Structures of thermophilic and mesophilic adenylate kinases from the genus Methanococcus. , 2003, Journal of molecular biology.

[208]  A. Sali,et al.  Comparative protein structure modeling by iterative alignment, model building and model assessment. , 2003, Nucleic Acids Research.

[209]  Xavier Robert,et al.  ESPript/ENDscript: extracting and rendering sequence and 3D information from atomic structures of proteins , 2003, Nucleic Acids Res..

[210]  Janusz M. Bujnicki,et al.  GeneSilico protein structure prediction meta-server , 2003, Nucleic Acids Res..

[211]  N. Dixon,et al.  Flexibility revealed by the 1.85 A crystal structure of the beta sliding-clamp subunit of Escherichia coli DNA polymerase III. , 2003, Acta crystallographica. Section D, Biological crystallography.

[212]  Dan S. Tawfik,et al.  Conformational diversity and protein evolution--a 60-year-old hypothesis revisited. , 2003, Trends in biochemical sciences.

[213]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[214]  Gustavo Caetano-Anollés,et al.  An evolutionarily structured universe of protein architecture. , 2003, Genome research.

[215]  Takashi Yamane,et al.  An empirical approach for structure-based prediction of carbohydrate-binding sites on proteins. , 2003, Protein engineering.

[216]  V. Metelev,et al.  PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. , 2003, Journal of molecular biology.

[217]  M. Onozuka,et al.  Steady-state kinetics and mutational studies of recombinant human thiamin pyrophosphokinase. , 2003, Journal of nutritional science and vitaminology.

[218]  T. Allers,et al.  Genetic analysis of homologous recombination in Archaea: Haloferax volcanii as a model organism. , 2003, Biochemical Society transactions.

[219]  T. Holman,et al.  Spectroscopic characterization of soybean lipoxygenase-1 mutants: the role of second coordination sphere residues in the regulation of enzyme activity. , 2003, Biochemistry.

[220]  Homme W Hellinga,et al.  An empirical model for electrostatic interactions in proteins incorporating multiple geometry‐dependent dielectric constants , 2003, Proteins.

[221]  L. Holm,et al.  Exhaustive enumeration of protein domain families. , 2003, Journal of molecular biology.

[222]  Paul W. Fitzjohn,et al.  In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling. , 2003, Journal of molecular biology.

[223]  S. M. Cowsik,et al.  Large contact surface interactions between proteins detected by time series analysis methods: Case study on C‐phycocyanins , 2003, Proteins.

[224]  A. Elofsson,et al.  Can correct protein models be identified? , 2003, Protein science : a publication of the Protein Society.

[225]  Liam J. McGuffin,et al.  Improvement of the GenTHREADER Method for Genomic Fold Recognition , 2003, Bioinform..

[226]  E. Gouaux,et al.  Probing the function, conformational plasticity, and dimer-dimer contacts of the GluR2 ligand-binding core: studies of 5-substituted willardiines and GluR2 S1S2 in the crystal. , 2003, Biochemistry.

[227]  Adam Godzik,et al.  XOL-1, primary determinant of sexual fate in C. elegans, is a GHMP kinase family member and a structural prototype for a class of developmental regulators. , 2003, Genes & development.

[228]  J. Heitman,et al.  A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. , 2003, Nucleic acids research.

[229]  D. Oesterhelt,et al.  Crystal structure of halophilic dodecin: a novel, dodecameric flavin binding protein from Halobacterium salinarum. , 2003, Structure.

[230]  Y. Ishino,et al.  Intermolecular ion pairs maintain the toroidal structure of Pyrococcus furiosus PCNA , 2003, Protein science : a publication of the Protein Society.

[231]  R. Garry,et al.  Proteomics computational analyses suggest that hepatitis C virus E1 and pestivirus E2 envelope glycoproteins are truncated class II fusion proteins. , 2003, Virology.

[232]  J. Sacchettini,et al.  Crystal Structure of ATP Phosphoribosyltransferase fromMycobacterium tuberculosis * , 2003, The Journal of Biological Chemistry.

[233]  J. Foote.  Isomeric Antibodies , 2003, Science.

[234]  Dan S. Tawfik,et al.  Antibody Multispecificity Mediated by Conformational Diversity , 2003, Science.

[235]  Virginijus Siksnys,et al.  The metal-independent type IIs restriction enzyme BfiI is a dimer that binds two DNA sites but has only one catalytic centre. , 2003, Journal of molecular biology.

[236]  J. Xiang,et al.  Mapping protein: carbohydrate interactions. , 2003, Current protein & peptide science.

[237]  P. Røgen,et al.  Automatic classification of protein structure by using Gauss integrals , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[238]  I. Kobayashi,et al.  A DNA Methyltransferase Can Protect the Genome from Postdisturbance Attack by a Restriction-Modification Gene Complex , 2002, Journal of bacteriology.

[239]  Hui Lu,et al.  MULTIPROSPECTOR: An algorithm for the prediction of protein–protein interactions by multimeric threading , 2002, Proteins.

[240]  Frances M. G. Pearl,et al.  Quantifying the similarities within fold space. , 2002, Journal of molecular biology.

[241]  V. D'souza,et al.  Structurally distinct active sites in the copper(II)-substituted aminopeptidases from Aeromonas proteolytica and Escherichia coli. , 2002, Journal of the American Chemical Society.

[242]  G. Schenk,et al.  Reactivity of M(II) metal-substituted derivatives of pig purple acid phosphatase (uteroferrin) with phosphate. , 2002, Inorganic chemistry.

[243]  D. Covell,et al.  Molecular motions and conformational changes of HPPK , 2002, Proteins.

[244]  S. Ciurli,et al.  New insights into the mechanism of purple acid phosphatase through (1)H NMR spectroscopy of the recombinant human enzyme. , 2002, Journal of the American Chemical Society.

[245]  Brian J. Smith,et al.  The trypanosomal trans-sialidase: two catalytic functions associated with one catalytic site. , 2002, Structure.

[246]  Marcin Feder,et al.  Structure Prediction and Phylogenetic Analysis of a Functionally Diverse Family of Proteins Homologous to the MT-A70 Subunit of the Human mRNA:m6A Methyltransferase , 2002, Journal of Molecular Evolution.

[247]  B. Poolman,et al.  ABC transporters: one, two or four extracytoplasmic substrate‐binding sites? , 2002, EMBO reports.

[248]  Sarah A. Teichmann,et al.  Principles of protein-protein interactions , 2002, ECCB.

[249]  R. Kraft,et al.  EcoRII: a restriction enzyme evolving recombination functions? , 2002, The EMBO journal.

[250]  E. Eisenstein,et al.  Structure of 2C‐methyl‐D‐erythrol‐2,4‐cyclodiphosphate synthase from Haemophilus influenzae: Activation by conformational transition , 2002, Proteins.

[251]  M. Gerstein,et al.  Genomic analysis of membrane protein families: abundance and conserved motifs , 2002, Genome Biology.

[252]  Mark Gerstein,et al.  Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic , 2002, Proteins.

[253]  D. Fong,et al.  Substrate promiscuity of an aminoglycoside antibiotic resistance enzyme via target mimicry. , 2002, The EMBO journal.

[254]  A. Sali,et al.  Comparative protein structure modeling of genes and genomes. , 2000, Annual review of biophysics and biomolecular structure.

[255]  I. Simon,et al.  Protein stability indicates divergent evolution of PD‐(D/E)XK type II restriction endonucleases , 2002, Protein science : a publication of the Protein Society.

[256]  Ozlem Keskin,et al.  Relating molecular flexibility to function: a case study of tubulin. , 2002, Biophysical journal.

[257]  J. Feigon,et al.  Solution structures of UBA domains reveal a conserved hydrophobic surface for protein-protein interactions. , 2002, Journal of molecular biology.

[258]  F. Penin,et al.  Topological changes in the transmembrane domains of hepatitis C virus envelope glycoproteins , 2002, The EMBO journal.

[259]  H. Kunte,et al.  New Type of Osmoregulated Solute Transporter Identified in Halophilic Members of the Bacteria Domain: TRAP Transporter TeaABC Mediates Uptake of Ectoine and Hydroxyectoine in Halomonas elongata DSM 2581T , 2002, Journal of bacteriology.

[260]  R. Varadarajan,et al.  Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. , 2002, Biochemistry.

[261]  S. Petersen,et al.  L-phenylalanine binding and domain organization in human phenylalanine hydroxylase: a differential scanning calorimetry study. , 2002, Biochemistry.

[262]  Jian Wang,et al.  A complete sequence of the T. tengcongensis genome. , 2002, Genome research.

[263]  Sherry L. Mowbray,et al.  Hinge-bending Motion of d-Allose-binding Protein from Escherichia coli , 2002, The Journal of Biological Chemistry.

[264]  J. Bujnicki,et al.  Evolutionary Relationship between Different Subgroups of Restriction Endonucleases* , 2002, The Journal of Biological Chemistry.

[265]  D. Lőrinczy,et al.  Effect of adenosine 5′‐[β,γ‐imido]triphosphate on myosin head domain movements , 2002 .

[266]  Virander S. Chauhan,et al.  Dehydrophenylalanine zippers: strong helix-helix clamping through a network of weak interactions. , 2002, Protein engineering.

[267]  Alfredo Colosimo,et al.  Nonlinear signal analysis methods in the elucidation of protein sequence-structure relationships. , 2002, Chemical reviews.

[268]  L. Que,et al.  Electro-nuclear double resonance spectroscopic evidence for a hydroxo-bridge nucleophile involved in catalysis by a dinuclear hydrolase. , 2002, Journal of the American Chemical Society.

[269]  Janusz M Bujnicki,et al.  Sequence permutations in the molecular evolution of DNA methyltransferases , 2002, BMC Evolutionary Biology.

[270]  D. Herschlag,et al.  Alkaline Phosphatase Revisited:  Hydrolysis of Alkyl Phosphates †. , 2002, Biochemistry.

[271]  O. Kohlbacher,et al.  Lectin-sugar interaction. Calculated versus experimental binding energies. , 2002, European journal of biochemistry.

[272]  András Fiser,et al.  Molecular Biophysics , 2022 .

[273]  A. Valencia,et al.  Prediction of protein--protein interaction sites in heterocomplexes with neural networks. , 2002, European journal of biochemistry.

[274]  B. Charloteaux,et al.  Analysis of the C-Terminal Membrane Anchor Domains of Hepatitis C Virus Glycoproteins E1 and E2: toward a Topological Model , 2002, Journal of Virology.

[275]  R. Huber,et al.  Crystal structure of the Bse634I restriction endonuclease: comparison of two enzymes recognizing the same DNA sequence. , 2002, Nucleic acids research.

[276]  N. Gormley,et al.  Many Type IIs Restriction Endonucleases Interact with Two Recognition Sites before Cleaving DNA* , 2002, The Journal of Biological Chemistry.

[277]  Alessandro Giuliani,et al.  Recurrence quantification analysis reveals interaction partners in paramyxoviridae envelope glycoproteins , 2002, Proteins.

[278]  H. Wolfson,et al.  Multiple diverse ligands binding at a single protein site : A matter of pre-existing populations , 2001 .

[279]  Golan Yona,et al.  Within the twilight zone: a sensitive profile-profile comparison tool based on information theory. , 2002, Journal of molecular biology.

[280]  J. Dixon,et al.  A Unique Carbohydrate Binding Domain Targets the Lafora Disease Phosphatase to Glycogen* , 2002, The Journal of Biological Chemistry.

[281]  G. Unden,et al.  C4-dicarboxylate carriers and sensors in bacteria. , 2002, Biochimica et biophysica acta.

[282]  R L Jernigan,et al.  Molecular mechanisms of chaperonin GroEL-GroES function. , 2002, Biochemistry.

[283]  Frances M. G. Pearl,et al.  The CATH protein family database: A resource for structural and functional annotation of genomes , 2002, Proteomics.

[284]  T. Kuzuyama.  Mevalonate and Nonmevalonate Pathways for the Biosynthesis of Isoprene Units , 2002, Bioscience, biotechnology, and biochemistry.

[285]  B. Poolman,et al.  On the osmotic signal and osmosensing mechanism of an ABC transport system for glycine betaine , 2001, The EMBO journal.

[286]  Marc A. Martí-Renom,et al.  EVA: continuous automatic evaluation of protein structure prediction servers , 2001, Bioinform..

[287]  E. Flores,et al.  Identification of genes encoding amino acid permeases by inactivation of selected ORFs from the Synechocystis genomic sequence. , 2001, Genome research.

[288]  D. Lörinczy,et al.  Nucleotide binding induces global and local structural changes of myosin head in muscle fibres. , 2001, European journal of biochemistry.

[289]  R. Woods,et al.  Involvement of water in carbohydrate-protein binding. , 2001, Journal of the American Chemical Society.

[290]  J Lundström,et al.  Pcons: A neural‐network–based consensus predictor that improves fold recognition , 2001, Protein science : a publication of the Protein Society.

[291]  R. Stevens,et al.  Global Efforts in Structural Genomics , 2001, Science.

[292]  J. Denu,et al.  Molecular reactions of protein phosphatases--insights from structure and chemistry. , 2001, Chemical reviews.

[293]  K. Wilson,et al.  Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism , 2001, JBIC Journal of Biological Inorganic Chemistry.

[294]  P. S. Kim,et al.  Design of potent inhibitors of HIV-1 entry from the gp41 N-peptide region , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[295]  I. Kobayashi.  Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. , 2001, Nucleic acids research.

[296]  A. Costantino,et al.  Mutagenesis of hepatitis C virus E1 protein affects its membrane-permeabilizing activity. , 2001, The Journal of general virology.

[297]  Nathan A. Baker,et al.  Electrostatics of nanosystems: Application to microtubules and the ribosome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[298]  Alessandro Senes,et al.  The Cα—H⋅⋅⋅O hydrogen bond: A determinant of stability and specificity in transmembrane helix interactions , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[299]  Thomas L. Madden,et al.  Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. , 2001, Nucleic acids research.

[300]  Robert A. Harris,et al.  Crystal structure of thiamin pyrophosphokinase. , 2001, Journal of molecular biology.

[301]  A. Pingoud,et al.  Sau3AI, a Monomeric Type II Restriction Endonuclease That Dimerizes on the DNA and Thereby Induces DNA Loops* , 2001, The Journal of Biological Chemistry.

[302]  T L Blundell,et al.  FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. , 2001, Journal of molecular biology.

[303]  K. Nishikawa,et al.  Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. , 2001, Journal of molecular biology.

[304]  Robert A. Harris,et al.  The crystal structure of yeast thiamin pyrophosphokinase. , 2001, Structure.

[305]  G. Schenk,et al.  A Purple Acid Phosphatase from Sweet Potato Contains an Antiferromagnetically Coupled Binuclear Fe-Mn Center* 210 , 2001, The Journal of Biological Chemistry.

[306]  Jozef Van Beeumen,et al.  The Highly Exposed Loop Region in Mammalian Purple Acid Phosphatase Controls the Catalytic Activity , 2001, Chembiochem : a European journal of chemical biology.

[307]  N. Grishin.  Fold change in evolution of protein structures. , 2001, Journal of structural biology.

[308]  A. Elcock,et al.  Identification of protein oligomerization states by analysis of interface conservation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[309]  Adam Godzik,et al.  Clustering of highly homologous sequences to reduce the size of large protein databases , 2001, Bioinform..

[310]  C. Vieille,et al.  Hyperthermophilic Enzymes: Sources, Uses, and Molecular Mechanisms for Thermostability , 2001, Microbiology and Molecular Biology Reviews.

[311]  N. Veljkovic,et al.  AIDS epidemic at the beginning of the third millennium: time for a new AIDS vaccine strategy. , 2001, Vaccine.

[312]  D. Moras,et al.  Dissecting the interaction network of multiprotein complexes by pairwise coexpression of subunits in E. coli. , 2001, Journal of molecular biology.

[313]  F. Quiocho,et al.  Trapping the transition state of an ATP-binding cassette transporter: evidence for a concerted mechanism of maltose transport. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[314]  E V Koonin,et al.  Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. , 2001, Genome research.

[315]  D Fischer,et al.  LiveBench‐1: Continuous benchmarking of protein structure prediction servers , 2001, Protein science : a publication of the Protein Society.

[316]  Y. Ishino,et al.  Crystal structure of an archaeal DNA sliding clamp: Proliferating cell nuclear antigen from Pyrococcus furiosus , 2001, Protein science : a publication of the Protein Society.

[317]  I Uchiyama,et al.  Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. , 2000, Gene.

[318]  A. Rosenzweig,et al.  Structure of the bacteriophage lambda Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes. , 2000, Biochemistry.

[319]  C. Haynes,et al.  Analysis of binding of the family 2a carbohydrate-binding module from Cellulomonas fimi xylanase 10A to cellulose: specificity and identification of functionally important amino acid residues. , 2000, Protein engineering.

[320]  Stephen K. Burley,et al.  An overview of structural genomics , 2000, Nature Structural Biology.

[321]  D. Hume,et al.  Structure, function, and regulation of tartrate-resistant acid phosphatase. , 2000, Bone.

[322]  N. Kannan,et al.  Aromatic clusters: a determinant of thermal stability of thermophilic proteins. , 2000, Protein engineering.

[323]  A. Sali,et al.  Protein structure modeling for structural genomics , 2000, Nature Structural Biology.

[324]  K. Rao,et al.  Maturation of an antibody response is governed by modulations in flexibility of the antigen-combining site. , 2000, Immunity.

[325]  I. Kobayashi,et al.  Evolution of sequence recognition by restriction-modification enzymes: selective pressure for specificity decrease. , 2000, Molecular biology and evolution.

[326]  G. Unden,et al.  Transport of C 4-Dicarboxylates in Wolinella succinogenes , 2000 .

[327]  G. Besra,et al.  Polyprenyl Phosphate Biosynthesis inMycobacterium tuberculosis and Mycobacterium smegmatis , 2000, Journal of bacteriology.

[328]  V. Šikšnys,et al.  Novel Subtype of Type IIs Restriction Enzymes , 2000, The Journal of Biological Chemistry.

[329]  Y. Sanejouand,et al.  Building‐block approach for determining low‐frequency normal modes of macromolecules , 2000, Proteins.

[330]  A. Rodríguez‐Romero,et al.  Stereochemical metrics of lectin-carbohydrate interactions: comparison with protein-protein interfaces. , 2000, Glycobiology.

[331]  Honggao Yan,et al.  Catalytic center assembly of HPPK as revealed by the crystal structure of a ternary complex at 1.25 A resolution. , 2000, Structure.

[332]  D. Hume,et al.  Purple acid phosphatases from bacteria: similarities to mammalian and plant enzymes. , 2000, Gene.

[333]  E V Koonin,et al.  SURVEY AND SUMMARY: holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. , 2000, Nucleic acids research.

[334]  Yoshihiro Kawaoka,et al.  Early Alterations of the Receptor-Binding Properties of H1, H2, and H3 Avian Influenza Virus Hemagglutinins after Their Introduction into Mammals , 2000, Journal of Virology.

[335]  A. Edwards,et al.  Structure-based functional classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum. , 2000, Journal of molecular biology.

[336]  R. Huber,et al.  Structure of the tetrameric restriction endonuclease NgoMIV in complex with cleaved DNA , 2000, Nature Structural Biology.

[337]  G J Barton,et al.  Application of multiple sequence alignment profiles to improve protein secondary structure prediction , 2000, Proteins.

[338]  M. Blaser,et al.  Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[339]  L. Que,et al.  Spectroscopic Characterization of a Ternary Phosphatase−Substrate−Fluoride Complex. Mechanistic Implications for Dinuclear Hydrolases [J. Am. Chem. Soc. 1999, 121, 9235−9236]. , 2000 .

[340]  Thomas C. Terwilliger,et al.  Electronic Reprint Biological Crystallography Maximum-likelihood Density Modification , 2022 .

[341]  G. Air,et al.  Influenza virus infection of desialylated cells. , 2000, Glycobiology.

[342]  J. M. Sauder,et al.  Large‐scale comparison of protein sequence alignment algorithms with structure alignments , 2000, Proteins.

[343]  E V Koonin,et al.  Estimating the number of protein folds and families from complete genome data. , 2000, Journal of molecular biology.

[344]  M. D. Topal,et al.  Crystal structure of NaeI—an evolutionary bridge between DNA endonuclease and topoisomerase , 2000, The EMBO journal.

[345]  F. Cohen,et al.  Co-evolution of proteins with their interaction partners. , 2000, Journal of molecular biology.

[346]  M. Blaser,et al.  Purification of the Novel Endonuclease, Hpy188I, and Cloning of Its Restriction-Modification Genes Reveal Evidence of Its Horizontal Transfer to the Helicobacter pylori Genome* , 2000, The Journal of Biological Chemistry.

[347]  M. Sternberg,et al.  Enhanced genome annotation using structural profiles in the program 3D-PSSM. , 2000, Journal of molecular biology.

[348]  D. Hume,et al.  Identification of mammalian-like purple acid phosphatases in a wide range of plants. , 2000, Gene.

[349]  S. Halford,et al.  Alternative geometries of DNA looping: an analysis using the SfiI endonuclease. , 2000, Journal of molecular biology.

[350]  A. Szilágyi,et al.  Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. , 2000, Structure.

[351]  D. Madern,et al.  Halophilic adaptation of enzymes , 2000, Extremophiles.

[352]  R. Jernigan,et al.  Proteins with similar architecture exhibit similar large-scale dynamic behavior. , 2000, Biophysical journal.

[353]  Liam J. McGuffin,et al.  The PSIPRED protein structure prediction server , 2000, Bioinform..

[354]  J Kuriyan,et al.  Crystal structure of the DNA polymerase processivity factor of T4 bacteriophage. , 2000, Journal of molecular biology.

[355]  B. Matthews,et al.  Structure and function of the methionine aminopeptidases. , 2000, Biochimica et biophysica acta.

[356]  R. Nussinov,et al.  Factors enhancing protein thermostability. , 2000, Protein engineering.

[357]  M. Teplova,et al.  Complexes of smooth muscle tropomyosin with F-actin studied by differential scanning calorimetry. , 2000, European journal of biochemistry.

[358]  Nello Cristianini,et al.  An Introduction to Support Vector Machines and Other Kernel-based Learning Methods , 2000 .

[359]  Frances M. G. Pearl,et al.  The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues. , 2000, Protein engineering.

[360]  P. Simpson,et al.  Trp22, Trp24, and Tyr8 play a pivotal role in the binding of the family 10 cellulose-binding module from Pseudomonas xylanase A to insoluble ligands. , 2000, Biochemistry.

[361]  D. Madern,et al.  Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui. , 2000, Biochemistry.

[362]  J M Thornton,et al.  Analysis and prediction of carbohydrate binding sites. , 2000, Protein engineering.

[363]  P. Simpson,et al.  Solution structure of the CBM10 cellulose binding module from Pseudomonas xylanase A. , 2000, Biochemistry.

[364]  N. Blom,et al.  Sequence and structure-based prediction of eukaryotic protein phosphorylation sites. , 1999, Journal of molecular biology.

[365]  D Fischer,et al.  Hybrid fold recognition: combining sequence derived properties with evolutionary information. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

[366]  I. Bahar,et al.  Structure‐based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X‐ray diffraction and NMR relaxation data , 1999, Proteins.

[367]  M. Saier,et al.  TRAP transporters: an ancient family of extracytoplasmic solute-receptor-dependent secondary active transporters. , 1999, Microbiology.

[368]  L. Wyns,et al.  The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: A comparative thermostability structural analysis of ten different TIM structures , 1999, Proteins.

[369]  M. Gromiha,et al.  Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. , 1999, Biophysical chemistry.

[370]  H. Toh,et al.  Functional Interactions of a Homolog of Proliferating Cell Nuclear Antigen with DNA Polymerases inArchaea , 1999, Journal of bacteriology.

[371]  I. Searle,et al.  Binuclear metal centers in plant purple acid phosphatases: Fe-Mn in sweet potato and Fe-Zn in soybean. , 1999, Archives of biochemistry and biophysics.

[372]  W. Eisenreich,et al.  Cytidine 5'-triphosphate-dependent biosynthesis of isoprenoids: YgbP protein of Escherichia coli catalyzes the formation of 4-diphosphocytidyl-2-C-methylerythritol. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[373]  J. Pflugrath,et al.  The finer things in X-ray diffraction data collection. , 1999, Acta crystallographica. Section D, Biological crystallography.

[374]  E. Johansson,et al.  Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center. , 1999, Journal of molecular biology.

[375]  C Urbanke,et al.  The Cfr10I restriction enzyme is functional as a tetramer. , 1999, Journal of molecular biology.

[376]  H. Lichtenthaler,et al.  Inhibitors of the nonmevalonate pathway of isoprenoid biosynthesis as antimalarial drugs. , 1999, Science.

[377]  S. Levy,et al.  Functional Analysis of Cell Surface-Expressed Hepatitis C Virus E2 Glycoprotein , 1999, Journal of Virology.

[378]  F. Barras,et al.  Functional Analysis of the Carbohydrate-Binding Domains of Erwinia chrysanthemi Cel5 (Endoglucanase Z) and an Escherichia coli Putative Chitinase , 1999, Journal of bacteriology.

[379]  M. Merkx,et al.  Fluoride inhibition of bovine spleen purple acid phosphatase: characterization of a ternary enzyme-phosphate-fluoride complex as a model for the active enzyme-substrate-hydroxide complex. , 1999, Biochemistry.

[380]  D. Hume,et al.  Crystal structure of mammalian purple acid phosphatase. , 1999, Structure.

[381]  M. Merkx,et al.  Evidence for nonbridged coordination of p-nitrophenyl phosphate to the dinuclear Fe(III)-M(II) center in bovine spleen purple acid phosphatase during enzymatic turnover. , 1999, Biochemistry.

[382]  T. Terwilliger,et al.  Rapid protein-folding assay using green fluorescent protein , 1999, Nature Biotechnology.

[383]  G. Zaccai,et al.  Relative role of anions and cations in the stabilization of halophilic malate dehydrogenase. , 1999, Biochemistry.

[384]  I. Zhulin,et al.  PAS Domains: Internal Sensors of Oxygen, Redox Potential, and Light , 1999, Microbiology and Molecular Biology Reviews.

[385]  Ruben Recabarren,et al.  Estimating the total number of protein folds , 1999, Proteins.

[386]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[387]  David C. Jones,et al.  GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.

[388]  T. Duke,et al.  Molecular model of muscle contraction. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[389]  R. Kappl,et al.  The active site of purple acid phosphatase from sweet potatoes (Ipomoea batatas) metal content and spectroscopic characterization. , 1999, European journal of biochemistry.

[390]  D. Cruickshank,et al.  Remarks about protein structure precision. , 1999, Acta crystallographica. Section D, Biological crystallography.

[391]  K. Nishikawa,et al.  Domain dislocation: a change of core structure in periplasmic binding proteins in their evolutionary history. , 1999, Journal of molecular biology.

[392]  B. Schölkopf,et al.  Advances in kernel methods: support vector learning , 1999 .

[393]  R. Webster,et al.  The Surface Glycoproteins of H5 Influenza Viruses Isolated from Humans, Chickens, and Wild Aquatic Birds Have Distinguishable Properties , 1999, Journal of Virology.

[394]  S E Brenner,et al.  Distribution of protein folds in the three superkingdoms of life. , 1999, Genome research.

[395]  C DeLisi,et al.  Estimating the number of protein folds. , 1998, Journal of molecular biology.

[396]  R. Jernigan,et al.  Identification of kinetically hot residues in proteins , 1998, Protein science : a publication of the Protein Society.

[397]  G. Böhm,et al.  The stability of proteins in extreme environments. , 1998, Current opinion in structural biology.

[398]  A. Sali,et al.  Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[399]  Eric Hunter,et al.  Potent suppression of HIV-1 replication in humans by T-20, a peptide inhibitor of gp41-mediated virus entry , 1998, Nature Medicine.

[400]  P. Qasba,et al.  Architecture of the sugar binding sites in carbohydrate binding proteins--a computer modeling study. , 1998, International journal of biological macromolecules.

[401]  K. Holmes.  A powerful stroke , 1998, Nature Structural Biology.

[402]  A. Costantino,et al.  Hepatitis C Virus E1 Protein Induces Modification of Membrane Permeability inE. coliCells , 1998 .

[403]  S. Phillips,et al.  Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence , 1998, The EMBO journal.

[404]  Roberto Dominguez,et al.  Crystal Structure of a Vertebrate Smooth Muscle Myosin Motor Domain and Its Complex with the Essential Light Chain Visualization of the Pre–Power Stroke State , 1998, Cell.

[405]  Yoshihiro Kawaoka,et al.  Molecular Basis for the Generation in Pigs of Influenza A Viruses with Pandemic Potential , 1998, Journal of Virology.

[406]  R J Read,et al.  Crystallography & NMR system: A new software suite for macromolecular structure determination. , 1998, Acta crystallographica. Section D, Biological crystallography.

[407]  P E Bourne,et al.  Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. , 1998, Protein engineering.

[408]  W. Eisenreich,et al.  The deoxyxylulose phosphate pathway of terpenoid biosynthesis in plants and microorganisms. , 1998, Chemistry & biology.

[409]  Z. X. Wang,et al.  A re-estimation for the total numbers of protein folds and superfamilies. , 1998, Protein engineering.

[410]  K. Karlsson.  Meaning and therapeutic potential of microbial recognition of host glycoconjugates , 1998, Molecular microbiology.

[411]  S. Hohmann,et al.  Thiamin metabolism and thiamin diphosphate-dependent enzymes in the yeast Saccharomyces cerevisiae: genetic regulation. , 1998, Biochimica et biophysica acta.

[412]  P. Simpson,et al.  All three surface tryptophans in Type IIa cellulose binding domains play a pivotal role in binding both soluble and insoluble ligands , 1998, FEBS letters.

[413]  S L Mowbray,et al.  Multiple open forms of ribose-binding protein trace the path of its conformational change. , 1998, Journal of molecular biology.

[414]  R. Huber,et al.  Structure-based redesign of the catalytic/metal binding site of Cfr10I restriction endonuclease reveals importance of spatial rather than sequence conservation of active centre residues. , 1998, Journal of molecular biology.

[415]  N. Sharon,et al.  Lectins: Carbohydrate-Specific Proteins That Mediate Cellular Recognition. , 1998, Chemical reviews.

[416]  V. Orlov,et al.  Differential scanning calorimetric studies on myosin and actin. , 1998, Biochemistry. Biokhimiia.

[417]  Winfried Boos,et al.  Maltose/Maltodextrin System of Escherichia coli: Transport, Metabolism, and Regulation , 1998, Microbiology and Molecular Biology Reviews.

[418]  E Warbrick,et al.  PCNA binding through a conserved motif. , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[419]  L R Pease,et al.  Structural basis of plasticity in T cell receptor recognition of a self peptide-MHC antigen. , 1998, Science.

[420]  U. Pieper,et al.  Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii. , 1998, Structure.

[421]  D. Covell,et al.  Correlation between native-state hydrogen exchange and cooperative residue fluctuations from a simple model. , 1998, Biochemistry.

[422]  E. Solomon,et al.  Circular Dichroism and Magnetic Circular Dichroism Studies of the Mixed-Valence Binuclear Non-Heme Iron Active Site in Uteroferrin and Its Anion Complexes , 1997 .

[423]  A. Vagin,et al.  MOLREP: an Automated Program for Molecular Replacement , 1997 .

[424]  B. Shaanan,et al.  Lectin-carbohydrate interactions: different folds, common recognition principles. , 1997, Trends in biochemical sciences.

[425]  D. Lipman,et al.  A genomic perspective on protein families. , 1997, Science.

[426]  R. Abagyan,et al.  Do aligned sequences share the same fold? , 1997, Journal of molecular biology.

[427]  R. Cooke,et al.  Opening of the myosin nucleotide triphosphate binding domain during the ATPase cycle. , 1997, Biochemistry.

[428]  J M Claverie,et al.  SAmBA: An interactive software for optimizing the design of biological macromolecules crystallization experiments , 1997, Proteins.

[429]  F. Giffhorn,et al.  Cloning, nucleotide sequence, and overexpression of smoS, a component of a novel operon encoding an ABC transporter and polyol dehydrogenases of Rhodobacter sphaeroides Si4 , 1997, Journal of bacteriology.

[430]  S. Jones,et al.  Prediction of protein-protein interaction sites using patch analysis. , 1997, Journal of molecular biology.

[431]  D. Kelly,et al.  TRAP transporters: a new family of periplasmic solute transport systems encoded by the dctPQM genes of Rhodobacter capsulatus and by homologs in diverse gram-negative bacteria , 1997, Journal of bacteriology.

[432]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[433]  David C. Jones,et al.  CATH--a hierarchic classification of protein domain structures. , 1997, Structure.

[434]  C. Zhang,et al.  Relations of the numbers of protein sequences, families and folds. , 1997, Protein engineering.

[435]  P Argos,et al.  Protein thermal stability, hydrogen bonds, and ion pairs. , 1997, Journal of molecular biology.

[436]  A. Atilgan,et al.  Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. , 1997, Folding & design.

[437]  C. Chothia,et al.  Population statistics of protein structures: lessons from structural classifications. , 1997, Current opinion in structural biology.

[438]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[439]  G. Schulz,et al.  Energy profile of maltooligosaccharide permeation through maltoporin as derived from the structure and from a statistical analysis of saccharide‐protein interactions , 1997, Protein science : a publication of the Protein Society.

[440]  C Kooperberg,et al.  Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. , 1997, Journal of molecular biology.

[441]  H. Berendsen,et al.  Model‐free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme , 1997, Proteins.

[442]  R Abagyan,et al.  A new method for modeling large‐scale rearrangements of protein domains , 1997, Proteins.

[443]  R. Huber,et al.  Thermodynamic stability of annexin V E17G: equilibrium parameters from an irreversible unfolding reaction. , 1997, Biochemistry.

[444]  Y. Hata,et al.  The crystal structure of zinc-containing ferredoxin from the thermoacidophilic archaeon Sulfolobus sp. strain 7. , 1997, Biochemistry.

[445]  Jörg Schwender,et al.  Biosynthesis of isoprenoids in higher plant chloroplasts proceeds via a mevalonate‐independent pathway , 1997, FEBS letters.

[446]  G. Desiraju.  The C-H×××O Hydrogen Bond: Structural Implications and Supramolecular Design , 1996 .

[447]  J. Lazovic,et al.  Selection of amino acid parameters for Fourier transform-based analysis of proteins , 1996, Comput. Appl. Biosci..

[448]  A. Driessen,et al.  Glutamate transport in Rhodobacter sphaeroides is mediated by a novel binding protein-dependent secondary transport system. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[449]  G. Charles Dismukes,et al.  Manganese Enzymes with Binuclear Active Sites. , 1996, Chemical reviews.

[450]  L. McIntosh,et al.  Probing the role of tryptophan residues in a cellulose‐binding domain by chemical modification , 1996, Protein science : a publication of the Protein Society.

[451]  W. Haase,et al.  Magnetic susceptibility studies on the diiron forms of the metalloprotein purple acid phosphate from bovine spleen and kidney bean , 1996 .

[452]  John Kuriyan,et al.  Structure of the C-Terminal Region of p21WAF1/CIP1 Complexed with Human PCNA , 1996, Cell.

[453]  Z. X. Wang,et al.  How many fold types of protein are there in nature? , 1996, Proteins.

[454]  W. Lipscomb,et al.  Two‐Metal Ion Catalysis in Enzymatic Acyl‐ and Phosphoryl‐Transfer Reactions , 1996 .

[455]  Tirion,et al.  Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis. , 1996, Physical review letters.

[456]  C Sander,et al.  Mapping the Protein Universe , 1996, Science.

[457]  G. Kleywegt.  Use of non-crystallographic symmetry in protein structure refinement. , 1996, Acta crystallographica. Section D, Biological crystallography.

[458]  R. Fröhlich,et al.  Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures. , 1996, Journal of molecular biology.

[459]  K. Nikaido,et al.  Liganded and Unliganded Receptors Interact with Equal Affinity with the Membrane Complex of Periplasmic Permeases, a Subfamily of Traffic ATPases* , 1996, The Journal of Biological Chemistry.

[460]  J. Schwender,et al.  Biosynthesis of isoprenoids (carotenoids, sterols, prenyl side-chains of chlorophylls and plastoquinone) via a novel pyruvate/glyceraldehyde 3-phosphate non-mevalonate pathway in the green alga Scenedesmus obliquus. , 1996, The Biochemical journal.

[461]  H. Schindelin,et al.  A left‐hand beta‐helix revealed by the crystal structure of a carbonic anhydrase from the archaeon Methanosarcina thermophila. , 1996, The EMBO journal.

[462]  J. Sussman,et al.  Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin , 1996, Nature Structural Biology.

[463]  M. Zółkiewski,et al.  Thermal unfolding of Acanthamoeba myosin II and skeletal muscle myosin. , 1996, Biophysical chemistry.

[464]  F. Quiocho,et al.  Atomic structure and specificity of bacterial periplasmic receptors for active transport and chemotaxis: variation of common themes , 1996, Molecular microbiology.

[465]  A. Shevchenko,et al.  Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels. , 1996, Analytical chemistry.

[466]  Michael Gribskov,et al.  Use of Receiver Operating Characteristic (ROC) Analysis to Evaluate Sequence Matching , 1996, Comput. Chem..

[467]  E. Querol,et al.  Analysis of protein conformational characteristics related to thermostability. , 1996, Protein engineering.

[468]  M Nayal,et al.  Valence screening of water in protein crystals reveals potential Na+ binding sites. , 1996, Journal of molecular biology.

[469]  R. Huber,et al.  Crystal structure of Citrobacter freundii restriction endonuclease Cfr10I at 2.15 A resolution. , 1996, Journal of molecular biology.

[470]  M. Hennig,et al.  2.0 A structure of indole-3-glycerol phosphate synthase from the hyperthermophile Sulfolobus solfataricus: possible determinants of protein stability. , 1995, Structure.

[471]  H. Fankhauser,et al.  Schizosaccharomyces pombe Thiamine Pyrophosphokinase Is Encoded by Gene tnr3 and Is a Regulator of Thiamine Metabolism, Phosphate Metabolism, Mating, and Growth (*) , 1995, The Journal of Biological Chemistry.

[472]  I. Kobayashi,et al.  Restriction-modification systems as genomic parasites in competition for specific sequences. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[473]  R. Blumenthal,et al.  Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. , 1995, Journal of molecular biology.

[474]  Virander S. Chauhan,et al.  First observation of an α-helix in α, β-dehydrooligopeptides: crystal structure of Boc-Val-ΔPhe-Ala-Leu-Gly-OMe , 1995 .

[475]  Z. Kelman,et al.  Structural and functional similarities of prokaryotic and eukaryotic DNA polymerase sliding clamps. , 1995, Nucleic acids research.

[476]  P. Tucker,et al.  Crystal structure of a purple acid phosphatase containing a dinuclear Fe(III)-Zn(II) active site. , 1995, Science.

[477]  S. Halford,et al.  The SfiI restriction endonuclease makes a four-strand DNA break at two copies of its recognition sequence. , 1995, Journal of molecular biology.

[478]  K. S. Yip,et al.  Insights into thermal stability from a comparison of the glutamate dehydrogenases from Pyrococcus furiosus and Thermococcus litoralis. , 1995, European journal of biochemistry.

[479]  S. Hamilton,et al.  Studies on the catalytic mechanism of pig purple acid phosphatase. , 1995, Archives of biochemistry and biophysics.

[480]  A G Murzin,et al.  SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.

[481]  A. Fisher,et al.  Structural studies of myosin:nucleotide complexes: a revised model for the molecular basis of muscle contraction. , 1995, Biophysical journal.

[482]  K. Hideg,et al.  A novel electron paramagnetic resonance spin label and its application to study the cross-bridge cycle. , 1995, Biophysical journal.

[483]  John Kuriyan,et al.  Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA , 1994, Cell.

[484]  David T. Jones,et al.  Protein superfamilles and domain superfolds , 1994, Nature.

[485]  K Watanabe,et al.  Multiple proline substitutions cumulatively thermostabilize Bacillus cereus ATCC7064 oligo-1,6-glucosidase. Irrefragable proof supporting the proline rule. , 1994, European journal of biochemistry.

[486]  R. Webster,et al.  Receptor specificity in human, avian, and equine H2 and H3 influenza virus isolates. , 1994, Virology.

[487]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[488]  E. Toone.  Structure and energetics of protein-carbohydrate complexes , 1994 .

[489]  S. Müller,et al.  Deceptive imprinting in the immune response against HIV-1. , 1994, Immunology today.

[490]  C. Bertozzi,et al.  The selectins and their ligands. , 1994, Current opinion in cell biology.

[491]  C. Sander,et al.  The FSSP database of structurally aligned protein fold families. , 1994, Nucleic acids research.

[492]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[493]  I. Dedova,et al.  Interaction of F‐actin with phosphate analogues studied by differential scanning calorimetry , 1994, FEBS letters.

[494]  S. Barondes,et al.  Galectins. Structure and function of a large family of animal lectins. , 1994, The Journal of biological chemistry.

[495]  R. Purcell,et al.  Sequence analysis of the core gene of 14 hepatitis C virus genotypes. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[496]  G. Pielak,et al.  Stability of yeast iso‐1‐ferricytochrome c as a function of pH and temperature , 1994, Protein science : a publication of the Protein Society.

[497]  J. Belágyi,et al.  ADP-induced changes in ordering of spin-labelled myosin heads in muscle fibres. , 1994, European journal of biochemistry.

[498]  Hansjörg Hoppe,et al.  Collectins — soluble proteins containing collagenous regions and lectin domains — and their roles in innate immunity , 1994, Protein science : a publication of the Protein Society.

[499]  A Kitao,et al.  Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis , 1994, Protein science : a publication of the Protein Society.

[500]  A. Plückthun,et al.  Protein folding in the periplasm of Escherichia coli , 1994, Molecular microbiology.

[501]  N N Alexandrov,et al.  Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins , 1994, Protein science : a publication of the Protein Society.

[502]  J. Thornton,et al.  Satisfying hydrogen bonding potential in proteins. , 1994, Journal of molecular biology.

[503]  E. Reisler,et al.  Dynamic properties of actin. Structural changes induced by beryllium fluoride. , 1994, The Journal of biological chemistry.

[504]  J. Navaza,et al.  AMoRe: an automated package for molecular replacement , 1994 .

[505]  G J Kleywegt,et al.  Detection, delineation, measurement and display of cavities in macromolecular structures. , 1994, Acta crystallographica. Section D, Biological crystallography.

[506]  D. Kilburn,et al.  The cellulose‐binding domain of endoglucanase A (CenA) from Cellulomonas fimi: evidence for the involvement of tryptophan residues in binding , 1994, Molecular microbiology.

[507]  I. Wilson,et al.  Structural evidence for induced fit as a mechanism for antibody-antigen recognition. , 1994, Science.

[508]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[509]  H. Berendsen,et al.  Essential dynamics of proteins , 1993, Proteins.

[510]  Wolfgang Kabsch,et al.  Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants , 1993 .

[511]  T. Matthews,et al.  A synthetic peptide from HIV-1 gp41 is a potent inhibitor of virus-mediated cell-cell fusion. , 1993, AIDS research and human retroviruses.

[512]  B. Matthews,et al.  Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme. , 1993, Biochemistry.

[513]  A. Bobkov,et al.  Calorimetric characterization of the stable complex of myosin subfragment 1 with ADP and beryllium fluoride , 1993, FEBS letters.

[514]  R H Purcell,et al.  At least 12 genotypes of hepatitis C virus predicted by sequence analysis of the putative E1 gene of isolates collected worldwide. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[515]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[516]  J. Paulson,et al.  Influenza virus strains selectively recognize sialyloligosaccharides on human respiratory epithelium; the role of the host cell in selection of hemagglutinin receptor specificity. , 1993, Virus research.

[517]  D. S. Moss,et al.  TLSANL: TLS parameter-analysis program for segmented anisotropic refinement of macromolecular structures , 1993 .

[518]  E. Egelman,et al.  A conformational change in the actin subunit can change the flexibility of the actin filament. , 1993, Journal of molecular biology.

[519]  R A Milligan,et al.  Structure of the actin-myosin complex and its implications for muscle contraction. , 1993, Science.

[520]  T. Blundell,et al.  Catching a common fold , 1993, Protein science : a publication of the Protein Society.

[521]  K S Wilson,et al.  The crystal structure of EcoRV endonuclease and of its complexes with cognate and non‐cognate DNA fragments. , 1993, The EMBO journal.

[522]  J. Knowles,et al.  Purple acid phosphatase: a diiron enzyme that catalyzes a direct phospho group transfer to water , 1993 .

[523]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[524]  J. Molkentin,et al.  The bovine mannose 6-phosphate/insulin-like growth factor II receptor. The role of arginine residues in mannose 6-phosphate binding. , 1993, The Journal of biological chemistry.

[525]  R. Hodges,et al.  Packing and hydrophobicity effects on protein folding and stability: Effects of β‐branched amino acids, valine and isoleucine, on the formation and stability of two‐stranded α‐helical coiled coils/leucine zippers , 1993, Protein science : a publication of the Protein Society.

[526]  R. Ezekowitz,et al.  Collectins: pattern recognition molecules involved in first line host defense. , 1993, Current opinion in immunology.

[527]  C. Pratesi,et al.  Solution structure of peptides containing two dehydro‐phenylalanine residues: A CD investigation , 1993, Biopolymers.

[528]  P. Kraulis,et al.  Investigation of the function of mutated cellulose‐binding domains of Trichoderma reesei cellobiohydrolase I , 1992, Proteins.

[529]  F. Quiocho,et al.  Crystallographic evidence of a large ligand-induced hinge-twist motion between the two domains of the maltodextrin binding protein involved in active transport and chemotaxis. , 1992, Biochemistry.

[530]  L. Lasky,et al.  Selectins: interpreters of cell-specific carbohydrate information during inflammation. , 1992, Science.

[531]  E. Egelman,et al.  Structural basis for the destabilization of F-actin by phosphate release following ATP hydrolysis. , 1992, Journal of molecular biology.

[532]  R. Hodges,et al.  Effect of trifluoroethanol on protein secondary structure: an NMR and CD study using a synthetic actin peptide. , 1992, Biochemistry.

[533]  A. Muhlrad,et al.  Characterization of stable beryllium fluoride, aluminum fluoride, and vanadate containing myosin subfragment 1-nucleotide complexes. , 1992, Biochemistry.

[534]  I. Karle,et al.  Folding, aggregation and molecular recognition in peptides. , 1992, Acta crystallographica. Section B, Structural science.

[535]  F A Quiocho,et al.  Atomic interactions in protein-carbohydrate complexes. Tryptophan residues in the periplasmic maltodextrin receptor for active transport and chemotaxis. , 1992, Journal of molecular biology.

[536]  C. Chothia.  One thousand families for the molecular biologist , 1992, Nature.

[537]  John Kuriyan,et al.  Three-dimensional structure of the β subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp , 1992, Cell.

[538]  J. Shaw,et al.  The mechanism of ligand binding to the periplasmic C4-dicarboxylate binding protein (DctP) from Rhodobacter capsulatus. , 1992, The Journal of biological chemistry.

[539]  H. Erickson,et al.  Kinetics of protein-protein association explained by Brownian dynamics computer simulation. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[540]  H. Nikaido,et al.  Mechanism of maltose transport in Escherichia coli: transmembrane signaling by periplasmic binding proteins. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[541]  D. Eisenberg,et al.  Assessment of protein models with three-dimensional profiles , 1992, Nature.

[542]  G. Piazzesi,et al.  Rapid regeneration of the actin-myosin power stroke in contracting muscle , 1992, Nature.

[543]  G. Andersson,et al.  Cloning, sequence, and developmental expression of a type 5, tartrate-resistant, acid phosphatase of rat bone. , 1991, The Journal of biological chemistry.

[544]  N. Vyas.  Atomic features of protein-carbohydrate interactions , 1991 .

[545]  S. David,et al.  Electrochemical properties of the diiron core of uteroferrin and its anion complexes. , 1991, Biochemistry.

[546]  A. Bairoch,et al.  The SWISS-PROT protein sequence data bank. , 1991, Nucleic acids research.

[547]  J. Zou,et al.  Improved methods for building protein models in electron density maps and the location of errors in these models. , 1991, Acta crystallographica. Section A, Foundations of crystallography.

[548]  M. Geeves.  The dynamics of actin and myosin association and the crossbridge model of muscle contraction. , 1991, The Biochemical journal.

[549]  P. Laggner,et al.  Conformational changes in bovine heart myosin as studied by EPR and DSC techniques. , 1990, General physiology and biophysics.

[550]  P. D. de Jong,et al.  Ligation-independent cloning of PCR products (LIC-PCR). , 1990, Nucleic acids research.

[551]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[552]  T. Tsong,et al.  Effects of ions and pH on the thermal stability of thin and thick filaments of skeletal muscle: high-sensitivity differential scanning calorimetric study. , 1990, Biochemistry.

[553]  V. Shnyrov,et al.  Domain structure of myosin subfragment-1. Selective denaturation of the 50 kDa segment. , 1990, FEBS letters.

[554]  M. Inouye,et al.  Enhancement of the thermostability of subtilisin E by introduction of a disulfide bond engineered on the basis of structural comparison with a thermophilic serine protease. , 1990, The Journal of biological chemistry.

[555]  G. N. Rogers,et al.  Receptor binding properties of human and animal H1 influenza virus isolates. , 1989, Virology.

[556]  P. V. von Hippel,et al.  Calculation of protein extinction coefficients from amino acid sequence data. , 1989, Analytical biochemistry.

[557]  J F Brandts,et al.  A simple model for proteins with interacting domains. Applications to scanning calorimetry data. , 1989, Biochemistry.

[558]  N. Sharon,et al.  Lectins as cell recognition molecules. , 1989, Science.

[559]  S. Halford,et al.  Discrimination between DNA sequences by the EcoRV restriction endonuclease. , 1989, Biochemistry.

[560]  Stefan Fischer,et al.  Stabilization of Actin Filaments by ATP and Inorganic Phosphate , 1989, Zeitschrift fur Naturforschung. C, Journal of biosciences.

[561]  R. Butterworth,et al.  Effect of Pyrithiamine Treatment and Subsequent Thiamine Rehabilitation on Regional Cerebral Amino Acids and Thiamine‐Dependent Enzymes , 1989, Journal of neurochemistry.

[562]  F. Quiocho.  Protein-carbohydrate interactions: basic molecular features , 1989 .

[563]  Wolfgang Kabsch,et al.  Evaluation of Single-Crystal X-ray Diffraction Data from a Position-Sensitive Detector , 1988 .

[564]  M. Carlier,et al.  Probing the mechanism of ATP hydrolysis on F-actin using vanadate and the structural analogs of phosphate BeF-3 and A1F-4. , 1988, The Journal of biological chemistry.

[565]  T. Hozumi.  Structural aspects of skeletal muscle F-actin as studied by tryptic digestion: evidence for a second nucleotide interacting site. , 1988, Journal of biochemistry.

[566]  M. Hendrich,et al.  Properties of the Fe(II)-Fe(III) derivative of red kidney bean purple phosphatase. Evidence for a binuclear zinc-iron center in the native enzyme , 1988 .

[567]  J. L. López-Lacomba,et al.  Differential scanning calorimetry of the irreversible thermal denaturation of thermolysin. , 1988, Biochemistry.

[568]  M. Carlier,et al.  Binding of phosphate to F-ADP-actin and role of F-ADP-Pi-actin in ATP-actin polymerization. , 1988, The Journal of biological chemistry.

[569]  James C. Davis,et al.  Spectroscopic and magnetic studies of the purple acid phosphatase from bovine spleen , 1987 .

[570]  I. Cosic,et al.  A novel method of protein analysis for prediction of biological function: application to tumor toxins. , 1987, Cancer biochemistry biophysics.

[571]  H. Baker,et al.  Structure of human lactoferrin at 3.2-A resolution. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[572]  A. Summors,et al.  Properties of a purple phosphatase from red kidney bean: a zinc-iron metalloenzyme , 1986 .

[573]  R. Roberts,et al.  The type 5, acid phosphatase from spleen of humans with hairy cell leukemia. Purification, properties, immunological characterization, and comparison with porcine uteroferrin. , 1985, The Journal of biological chemistry.

[574]  I. Cosic,et al.  Is it Possible to Analyze DNA and Protein Sequences by the Methods of Digital Signal Processing? , 1985, IEEE Transactions on Biomedical Engineering.

[575]  A. Muhlrad,et al.  Effect of mild heat treatment on the ATPase activity and proteolytic sensitivity of myosin subfragment-1. , 1984, Archives of biochemistry and biophysics.

[576]  B. Qiang,et al.  A type II restriction endonuclease with an eight nucleotide specificity from Streptomyces fimbriatus. , 1984, Nucleic acids research.

[577]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[578]  M. Karplus,et al.  Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[579]  M. Ishioroshi,et al.  Scanning Calorimetric Studies on Thermal Denaturation of Myosin and Its Subfragments , 1983 .

[580]  P. Aisen,et al.  Physical characterization of two-iron uteroferrin. Evidence for a spin-coupled binuclear iron cluster. , 1983, The Journal of biological chemistry.

[581]  G. Richarme.  Associative properties of the Escherichia coli galactose-binding protein and maltose-binding protein. , 1982, Biochimica et biophysica acta.

[582]  C. Stammer,et al.  The enzyme stability of dehydropeptides. , 1978, Biochemical and biophysical research communications.

[583]  J. de Jersey,et al.  Iron-containing acid phosphatases: comparison of the enzymes from beef spleen and pig allantoic fluid. , 1978, Biochemical and biophysical research communications.

[584]  D. Lancet,et al.  Kinetic evidence for hapten-induced conformational transition in immunoglobin MOPC 460. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[585]  W. Kabsch.  A solution for the best rotation to relate two sets of vectors , 1976 .

[586]  H. Larsen,et al.  Halobacterium volcanii spec. nov., a Dead Sea halobacterium with a moderate salt requirement , 1975, Archives of Microbiology.

[587]  J. Lanyi,et al.  Salt-dependent properties of proteins from extremely halophilic bacteria. , 1974, Bacteriological reviews.

[588]  V. Veljković,et al.  The dependence of the fermi energy on the atomic number , 1973 .

[589]  V. Veljković,et al.  Simple General-Model Pseudopotential , 1972 .

[590]  J. Eccleston,et al.  Elementary processes of the magnesium ion-dependent adenosine triphosphatase activity of heavy meromyosin. A transient kinetic approach to the study of kinases and adenosine triphosphatases and a colorimetric inorganic phosphate assay in situ. , 1972, The Biochemical journal.

[591]  F. B. Fuller.  The writhing number of a space curve. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[592]  D. Koshland.  Application of a Theory of Enzyme Specificity to Protein Synthesis. , 1958, Proceedings of the National Academy of Sciences of the United States of America.

[593]  A. Mandell,et al.  Designing allosteric peptide ligands targeting a globular protein. , 2007, Biopolymers.

[594]  A. Giuliani,et al.  Simulated point mutations in the Aalpha-chain of human fibrinogen support a role of the alphaC domain in the stabilization of fibrin gel. , 2006, Pathophysiology of haemostasis and thrombosis.

[595]  F. Rey,et al.  Virus membrane-fusion proteins: more than one way to make a hairpin , 2006, Nature Reviews Microbiology.

[596]  L. Guddat,et al.  Inhibition studies of purple acid phosphatases: implications for the catalytic mechanism , 2006 .

[597]  G. Thomas,et al.  Novel ligands for the extracellular solute receptors of two bacterial TRAP transporters. , 2006, Microbiology.

[598]  Alfredo Colosimo,et al.  Structure-Related Statistical Singularities along Protein Sequences: A Correlation Study , 2005, J. Chem. Inf. Model..

[599]  Janusz M Bujnicki,et al.  Generalized protein structure prediction based on combination of fold‐recognition with de novo folding and evaluation of models , 2005, Proteins.

[600]  Marcin Feder,et al.  FRankenstein becomes a cyborg: The automatic recombination and realignment of fold recognition models in CASP6 , 2005, Proteins.

[601]  J. Bao,et al.  Effect of amino acid residue and oligosaccharide chain chemical modifications on spectral and hemagglutinating activity of Millettia dielsiana Harms. ex Diels. lectin. , 2005, Acta biochimica et biophysica Sinica.

[602]  Č. Venclovas,et al.  Comparative modeling in CASP6 using consensus approach to template selection, sequence‐structure alignment, and structure assessment , 2005, Proteins.

[603]  Tim J. P. Hubbard,et al.  SCOP database in 2004: refinements integrate structure and sequence family data , 2004, Nucleic Acids Res..

[604]  Janusz M Bujnicki,et al.  Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily. , 2004, Nucleic acids research.

[605]  J. Bujnicki.  Molecular Phylogenetics of Restriction Endonucleases , 2004 .

[606]  J. Claverie,et al.  Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets , 2004, Journal of Structural and Functional Genomics.

[607]  B. Mikami,et al.  Structure and function of a hypothetical Pseudomonas aeruginosa protein PA1167 classified into family PL-7: a novel alginate lyase with a beta-sandwich fold. , 2004, The Journal of biological chemistry.

[608]  Peer Bork,et al.  SMART 4.0: towards genomic data integration , 2004, Nucleic Acids Res..

[609]  A. Kolinski.  Protein modeling and structure prediction with a reduced representation. , 2004, Acta biochimica Polonica.

[610]  James P J Chong,et al.  A novel nuclease-ATPase (Nar71) from archaea is part of a proposed thermophilic DNA repair system. , 2004, Nucleic acids research.

[611]  I. Kobayashi.  Restriction-Modification Systems as Minimal Forms of Life , 2004 .

[612]  S. Yokoyama,et al.  Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis. , 2003, Acta crystallographica. Section D, Biological crystallography.

[613]  Johanna M. Rommens,et al.  Mutations in SBDS are associated with Shwachman–Diamond syndrome , 2003, Nature Genetics.

[614]  Thomas C Terwilliger,et al.  SOLVE and RESOLVE: automated structure solution and density modification. , 2003, Methods in enzymology.

[615]  K. Ginalski,et al.  Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment , 2003, Proteins.

[616]  A. Sali,et al.  Modeller: generation and refinement of homology-based protein structure models. , 2003, Methods in enzymology.

[617]  Burkhard Rost,et al.  The PredictProtein server , 2003, Nucleic Acids Res..

[618]  Daniel Fischer,et al.  Twenty thousand ORFan microbial protein families for the biologist? , 2003, Structure.

[619]  S. Bell,et al.  A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. , 2003, Molecular cell.

[620]  Marcin Feder,et al.  A “FRankenstein's monster” approach to comparative modeling: Merging the finest fragments of Fold‐Recognition models and iterative model refinement aided by 3D structure evaluation , 2003, Proteins.

[621]  Richard J. Roberts,et al.  REBASE: restriction enzymes and methyltransferases , 2003, Nucleic Acids Res..

[622]  Anna Tramontano,et al.  Assessment of homology‐based predictions in CASP5 , 2003, Proteins.

[623]  Jonathan Casper,et al.  Combining local‐structure, fold‐recognition, and new fold methods for protein structure prediction , 2003, Proteins.

[624]  J. Frère,et al.  Substrate-activated zinc binding of metallo-beta -lactamases: physiological importance of mononuclear enzymes. , 2002, The Journal of biological chemistry.

[625]  S. Pongor,et al.  Protein fold similarity estimated by a probabilistic approach based on C(alpha)-C(alpha) distance comparison. , 2002, Journal of molecular biology.

[626]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[627]  Adam Godzik,et al.  Tolerating some redundancy significantly speeds up clustering of large protein databases , 2002, Bioinform..

[628]  M. Wink.  Medicinal Natural Products. A Biosynthetic Approach , 2002 .

[629]  John Moult,et al.  A unifold, mesofold, and superfold model of protein fold use , 2002, Proteins.

[630]  J. Bujnicki,et al.  Grouping together highly diverged PD-(D/E)XK nucleases and identification of novel superfamily members using structure-guided alignment of sequence profiles. , 2001, Journal of molecular microbiology and biotechnology.

[631]  R. Jernigan,et al.  Anisotropy of fluctuation dynamics of proteins with an elastic network model. , 2001, Biophysical journal.

[632]  J. Bujnicki,et al.  Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. , 2001, Acta biochimica Polonica.

[633]  A G Cochran,et al.  Tryptophan zippers: stable, monomeric beta -hairpins. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[634]  Y. Sanejouand,et al.  Conformational change of proteins arising from normal mode calculations. , 2001, Protein engineering.

[635]  J. Bujnicki,et al.  Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. , 2001, Trends in biochemical sciences.

[636]  D Fischer,et al.  LiveBench‐2: Large‐scale automated evaluation of protein structure prediction servers , 2001, Proteins.

[637]  J. Bujnicki.  A model of structure and action of Sau3AI restriction endonuclease that comprises two MutH-like endonuclease domains within a single polypeptide. , 2001, Acta microbiologica Polonica.

[638]  R. Kumar.  Preparation of genomic DNA from bacteria , 2001 .

[639]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[640]  Patrice Koehl,et al.  The ASTRAL compendium for protein structure and sequence analysis , 2000, Nucleic Acids Res..

[641]  E. Warbrick.  The puzzle of PCNA's many partners. , 2000, BioEssays : news and reviews in molecular, cellular and developmental biology.

[642]  Janusz M. Bujnicki,et al.  Phylogeny of the Restriction Endonuclease-Like Superfamily Inferred from Comparison of Protein Structures , 2000, Journal of Molecular Evolution.

[643]  Mindy I. Davis,et al.  Geometric and electronic structure/function correlations in non-heme iron enzymes. , 2000, Chemical reviews.

[644]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[645]  M Ouali,et al.  Cascaded multiple classifiers for secondary structure prediction , 2000, Protein science : a publication of the Protein Society.

[646]  M. Twitchett,et al.  Structure, properties and reactivity of the (FeFeIII)-Fe-II and (ZnFeIII)-Fe-II purple acid phosphatases , 1999 .

[647]  E. García-Hernández,et al.  Structural bases of lectin‐carbohydrate affinities: Comparison with protein‐folding energetics , 1999, Protein science : a publication of the Protein Society.

[648]  K. Nakai,et al.  PSORT: a program for detecting sorting signals in proteins and predicting their subcellular localization. , 1999, Trends in biochemical sciences.

[649]  Christopher M. Summa,et al.  De novo design and structural characterization of proteins and metalloproteins. , 1999, Annual review of biochemistry.

[650]  K C Holmes,et al.  Structural mechanism of muscle contraction. , 1999, Annual review of biochemistry.

[651]  A. Costantino,et al.  Hepatitis C virus E1 protein induces modification of membrane permeability in E. coli cells. , 1998, Virology.

[652]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[653]  G. Varani,et al.  RNA recognition by RNP proteins during RNA processing. , 1998, Annual review of biophysics and biomolecular structure.

[654]  L Serrano,et al.  Design of a 20-amino acid, three-stranded beta-sheet protein. , 1998, Science.

[655]  S. Halford,et al.  DNA excision by the Sfi I restriction endonuclease. , 1998, Journal of molecular biology.

[656]  D. Barford,et al.  The structure and mechanism of protein phosphatases: insights into catalysis and regulation. , 1998, Annual review of biophysics and biomolecular structure.

[657]  S. Halford,et al.  DNA looping by the Sfi I restriction endonuclease. , 1998, Journal of molecular biology.

[658]  R Sánchez,et al.  Evaluation of comparative protein structure modeling by MODELLER‐3 , 1997, Proteins.

[659]  G. Kleywegt,et al.  Detecting folding motifs and similarities in protein structures. , 1997, Methods in enzymology.

[660]  Z. Otwinowski,et al.  Processing of X-ray diffraction data collected in oscillation mode. , 1997, Methods in enzymology.

[661]  D. Wilcox.  Binuclear Metallohydrolases. , 1996, Chemical reviews.

[662]  W R Taylor,et al.  SSAP: sequential structure alignment program for protein structure comparison. , 1996, Methods in enzymology.

[663]  Virander S. Chauhan,et al.  Conformational characteristics of peptides containing alpha, beta-dehydroamino acid residues. , 1996, Biopolymers.

[664]  W. Weis,et al.  Structural basis of lectin-carbohydrate recognition. , 1996, Annual review of biochemistry.

[665]  D. W. Hayden,et al.  The mechanism of force generation in myosin: a disorder-to-order transition, coupled to internal structural changes. , 1995, Biophysical journal.

[666]  J. Rini,et al.  Lectin structure. , 1995, Annual review of biophysics and biomolecular structure.

[667]  N. Sharon,et al.  Lectins--proteins with a sweet tooth: functions in cell recognition. , 1995, Essays in biochemistry.

[668]  M. A. Aquino,et al.  Mechanism of the reaction of different phosphates with the iron(II)iron(III) form of purple acid phosphatase from porcine uteri (uteroferrin) , 1994 .

[669]  A. Sykes,et al.  Redox reactivity of the binuclear iron active site of porcine purple acid phosphatase (uteroferrin) , 1994 .

[670]  H. Gilbert,et al.  The role of conserved tryptophan residues in the interaction of a bacterial cellulose binding domain with its ligand. , 1993, FEMS microbiology letters.

[671]  Virander S. Chauhan,et al.  Solution conformation and synthesis of a linear heptapeptide containing two dehydrophenylalanine residues separated by three L-amino acids , 1990 .

[672]  N Go,et al.  A theorem on amplitudes of thermal atomic fluctuations in large molecules assuming specific conformations calculated by normal mode analysis. , 1990, Biophysical chemistry.

[673]  J. Schellman.  The thermodynamic stability of proteins. , 1987, Annual review of biophysics and biophysical chemistry.

[674]  J. Sturtevant.  Biochemical Applications of Differential Scanning Calorimetry , 1987 .

[675]  P. Privalov,et al.  Scanning microcalorimetry in studying temperature-induced changes in proteins. , 1986, Methods in enzymology.

[676]  L. Gierasch,et al.  Dehydrophenylalanine can occur in various reverse-turn sites: conformational analysis of delta Phe-containing model peptides. , 1986, Biopolymers.

[677]  Gaetano Granozzi,et al.  On the conformational flexibility of model compounds of β-substituted α, β-unsaturated peptides , 1982 .

[678]  V. Veljković,et al.  Theoretical prediction of mutagenicity and carcinogenicity of chemical substances. , 1976, Cancer biochemistry biophysics.

[679]  J. Norby.  Studies on a coupled enzyme assay for rate measurements of ATPase reactions. , 1971, Acta chemica Scandinavica.

[680]  F. Thomé‐Beau,et al.  [ATP:thiamine pyrophosphotransferase. Purification and a study of the reaction mechanism]. , 1969, Biochimica et biophysica acta.

[681]  M. Kreek,et al.  Sticky-End PCR : New Method for Subcloning , 2022 .