Computational Protein-Protein Interactions

Basic Principles of Protein-Protein Interaction, J. Janin Low-Resolution Recognition Factors Determine Major Characteristics of the Energy Landscape in Protein-Protein Interaction, I.A. Vakser The Molecular Architecture of Protein-Protein Binding Sites, E.J. Sundberg Mapping Protein Function by Combinatorial Mutagenesis, G. Pal and S.S. Sidhu The Association of Protein-Protein Complexes, G. Schreiber Computational Simulations of Protein-Protein and Protein-Nucleic Acid Association, G.V. Pachov, R.R. Gabdoulline, and R.C. Wade Computational Design of Protein-Protein Interactions, J.M. Shifman Protein-Protein Docking, H. Hwang, B. Pierce, and Z. Weng Prediction of Protein Interaction Sites, Y. Ofran Predicting Molecular Interactions in Structural Proteomics, I. Kufareva and R. Abagyan Rearrangements and Expansion of the Domain Content in Proteins Frequently Increase the Protein Connectivity in the Protein-Protein Interaction Network, I. Cohen-Gihon, R. Sharan, and R. Nussinov Intrinsically Disordered Proteins and Their Recognition Functions, V.N. Uversky, M. Fuxreiter, C.J. Oldfield, A.K. Dunker, and P. Tompa Identification of Druggable Hot Spots on Proteins and in Protein-Protein Interfaces, D. Beglov, R. Brenke, G.-Y. Chuang, D. Hall, M. Landon, C.H. Ngan, Y. Shen, S. Thiel, B. Zerbe, D. Kozakov, and S. Vajda Designing Protein-Protein Interaction Inhibitors, M. Montes Index

[1]  S. Teichmann,et al.  The relationship between domain duplication and recombination. , 2005, Journal of molecular biology.

[2]  Shoshana J Wodak,et al.  Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. , 2004, Current opinion in structural biology.

[3]  Miklós Vargyas,et al.  Making Real Molecules in Virtual Space , 2004 .

[4]  B. Shoichet,et al.  Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. , 2002, Journal of medicinal chemistry.

[5]  G. V. Paolini,et al.  Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes , 1997, J. Comput. Aided Mol. Des..

[6]  Michelle R. Arkin,et al.  Binding of small molecules to an adaptive protein–protein interface , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[7]  V. Uversky,et al.  Protein folding revisited. A polypeptide chain at the folding – misfolding – nonfolding cross-roads: which way to go? , 2003, Cellular and Molecular Life Sciences CMLS.

[8]  N. Kamiya,et al.  Rational discovery of a novel interface for a coactivator in the peroxisome proliferator‐activated receptor γ: Theoretical implications of impairment in type 2 diabetes mellitus , 2004, Proteins.

[9]  P. Tompa,et al.  Structural disorder throws new light on moonlighting. , 2005, Trends in biochemical sciences.

[10]  Toshiaki Hara,et al.  Structure of the Tfb1/p53 complex: Insights into the interaction between the p62/Tfb1 subunit of TFIIH and the activation domain of p53. , 2006, Molecular cell.

[11]  John Moult,et al.  Evaluation of disorder predictions in CASP5 , 2003, Proteins.

[12]  G. Rishton.  Nonleadlikeness and leadlikeness in biochemical screening. , 2003, Drug discovery today.

[13]  Jeremy L Jenkins,et al.  Virtual screening to enrich hit lists from high‐throughput screening: A case study on small‐molecule inhibitors of angiogenin , 2002, Proteins.

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

[15]  István Simon,et al.  Preformed structural elements feature in partner recognition by intrinsically unstructured proteins. , 2004, Journal of molecular biology.

[16]  D. Covell,et al.  A role for surface hydrophobicity in protein‐protein recognition , 1994, Protein science : a publication of the Protein Society.

[17]  Maxim Totrov,et al.  Improving CAPRI predictions: Optimized desolvation for rigid‐body docking , 2005, Proteins.

[18]  Thomas Sander,et al.  Toxicity-Indicating Structural Patterns , 2006, J. Chem. Inf. Model..

[19]  Jürgen Bajorath,et al.  Evaluation of Descriptors and Mini-Fingerprints for the Identification of Molecules with Similar Activity , 2000, J. Chem. Inf. Comput. Sci..

[20]  Ruth Nussinov,et al.  Predicting molecular interactions in silico: I. A guide to pharmacophore identification and its applications to drug design. , 2004, Current medicinal chemistry.

[21]  V. Uversky.  Intrinsically Disordered Proteins , 2000 .

[22]  E. Koonin,et al.  The Impact of Comparative Genomics on Our Understanding of Evolution , 2000, Cell.

[23]  A. Hamilton,et al.  Strategies for targeting protein-protein interactions with synthetic agents. , 2005, Angewandte Chemie.

[24]  Cheryl H Arrowsmith,et al.  Characterization of segments from the central region of BRCA1: an intrinsically disordered scaffold for multiple protein-protein and protein-DNA interactions? , 2005, Journal of molecular biology.

[25]  P. Argos.  An investigation of protein subunit and domain interfaces. , 1988, Protein engineering.

[26]  Christopher J. Oldfield,et al.  Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins. , 2007, Journal of proteome research.

[27]  Matthew P. Repasky,et al.  Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. , 2004, Journal of medicinal chemistry.

[28]  R. Woody,et al.  Circular dichroism. , 1995, Methods in enzymology.

[29]  R. Nussinov,et al.  Conservation of polar residues as hot spots at protein interfaces , 2000, Proteins.

[30]  Thierry Langer,et al.  Chemical feature-based pharmacophores and virtual library screening for discovery of new leads. , 2003, Current opinion in drug discovery & development.

[31]  A. Elofsson,et al.  What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? , 2006, Genome Biology.

[32]  Christopher J. Oldfield,et al.  Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling , 2005, Journal of molecular recognition : JMR.

[33]  R. Nussinov,et al.  Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design. , 2007, Current topics in medicinal chemistry.

[34]  Natasja Brooijmans,et al.  Molecular recognition and docking algorithms. , 2003, Annual review of biophysics and biomolecular structure.

[35]  B. Shoichet,et al.  High-throughput assays for promiscuous inhibitors , 2005, Nature chemical biology.

[36]  David Ozonoff,et al.  Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble , 2008, Chemical biology & drug design.

[37]  R. Abagyan,et al.  Soft protein–protein docking in internal coordinates , 2002, Protein science : a publication of the Protein Society.

[38]  S. Teichmann,et al.  Supra-domains: evolutionary units larger than single protein domains. , 2004, Journal of molecular biology.

[39]  Miklos Feher,et al.  Consensus scoring for protein-ligand interactions. , 2006, Drug discovery today.

[40]  K M Logan,et al.  Phe217 regulates the transfer of allosteric information across the subunit interface of the RecA protein filament. , 2001, Structure.

[41]  A. Fink.  Natively unfolded proteins. , 2005, Current opinion in structural biology.

[42]  Gerhard Klebe,et al.  Identification and Mapping of Small-Molecule Binding Sites in Proteins: Computational Tools for Structure-Based Drug Design. , 2002 .

[43]  S. Jones,et al.  Analysis of protein-protein interaction sites using surface patches. , 1997, Journal of molecular biology.

[44]  C. Lipinski.  Drug-like properties and the causes of poor solubility and poor permeability. , 2000, Journal of pharmacological and toxicological methods.

[45]  Zoran Obradovic,et al.  The protein trinity—linking function and disorder , 2001, Nature Biotechnology.

[46]  Christophe Cleva,et al.  Chemical substructures in drug discovery. , 2003, Drug discovery today.

[47]  Hoh,et al.  Neurofilament‐L homopolymers are less mechanically stable than native neurofilaments , 1998, Journal of microscopy.

[48]  P. Myung,et al.  2D-QSAR and HQSAR of the inhibition of calcineurin-NFAT signaling by blocking protein-protein interaction with N-(4-oxo-1 (4H)-naphthalenylidene)benzenesulfonamide analogues , 2007, Archives of pharmacal research.

[49]  S. Provencher,et al.  Estimation of globular protein secondary structure from circular dichroism. , 1981, Biochemistry.

[50]  W. Delano.  Unraveling hot spots in binding interfaces: progress and challenges. , 2002, Current opinion in structural biology.

[51]  Yuan-Ping Pang,et al.  EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases , 2001, J. Comput. Chem..

[52]  Burkhard Rost,et al.  NORSp: predictions of long regions without regular secondary structure , 2003, Nucleic Acids Res..

[53]  E. Egelman,et al.  Electron microscopy of RecA-DNA complexes: Two different states, their functional significance and relation to the solved crystal structure , 1993 .

[54]  F. Dahlquist,et al.  The C-terminal half of the anti-sigma factor FlgM contains a dynamic equilibrium solution structure favoring helical conformations. , 1998, Biochemistry.

[55]  M. Silberstein,et al.  Exploring the binding sites of the haloalkane dehalogenase DhlA from Xanthobacter autotrophicus GJ10. , 2007, Biochemistry.

[56]  Stephen Muggleton,et al.  Scaffold Hopping in Drug Discovery Using Inductive Logic Programming , 2008, J. Chem. Inf. Model..

[57]  H. Broughton,et al.  A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening. , 2000, Journal of molecular graphics & modelling.

[58]  A. Bender,et al.  Circular fingerprints: flexible molecular descriptors with applications from physical chemistry to ADME. , 2006, IDrugs : the investigational drugs journal.

[59]  Robert J. Jilek,et al.  "Lead hopping". Validation of topomer similarity as a superior predictor of similar biological activities. , 2004, Journal of medicinal chemistry.

[60]  H. Kubinyi.  Drug research: myths, hype and reality , 2003, Nature Reviews Drug Discovery.

[61]  Zoran Obradovic,et al.  Optimizing Long Intrinsic Disorder Predictors with Protein Evolutionary Information , 2005, J. Bioinform. Comput. Biol..

[62]  Thomas Lengauer,et al.  Evaluation of the FLEXX incremental construction algorithm for protein–ligand docking , 1999, Proteins.

[63]  M. Karplus,et al.  Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. , 1993, Journal of medicinal chemistry.

[64]  K. Schulten,et al.  Single-Molecule Experiments in Vitro and in Silico , 2007, Science.

[65]  L. Patthy,et al.  Exon shuffling and other ways of module exchange. , 1996, Matrix biology : journal of the International Society for Matrix Biology.

[66]  M J Sternberg,et al.  New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. , 1992, Journal of molecular biology.

[67]  Karl H. Clodfelter,et al.  Identification of substrate binding sites in enzymes by computational solvent mapping. , 2003, Journal of molecular biology.

[68]  Corinne J. Smith,et al.  Natively unfolded domains in endocytosis: hooks, lines and linkers , 2004, EMBO reports.

[69]  Sandor Vajda,et al.  Characterization of protein-ligand interaction sites using experimental and computational methods. , 2006, Current opinion in drug discovery & development.

[70]  S. Wuchty,et al.  Evolutionary cores of domain co-occurrence networks , 2005, BMC Evolutionary Biology.

[71]  C. Chothia,et al.  Evolution of the Protein Repertoire , 2003, Science.

[72]  Martin Stahl,et al.  Binding site characteristics in structure-based virtual screening: evaluation of current docking tools , 2003, Journal of molecular modeling.

[73]  Jürgen Bajorath,et al.  Design and Evaluation of a Molecular Fingerprint Involving the Transformation of Property Descriptor Values into a Binary Classification Scheme , 2003, J. Chem. Inf. Comput. Sci..

[74]  Nathan Brown,et al.  On scaffolds and hopping in medicinal chemistry. , 2006, Mini reviews in medicinal chemistry.

[75]  Alfonso Valencia,et al.  Prediction of protein-protein interactions from evolutionary information. , 2003, Methods of biochemical analysis.

[76]  J. Brosius.  The Contribution of RNAs and Retroposition to Evolutionary Novelties , 2003, Genetica.

[77]  A. Elofsson,et al.  Multi-domain proteins in the three kingdoms of life: orphan domains and other unassigned regions. , 2005, Journal of molecular biology.

[78]  H. Dyson,et al.  Unfolded proteins and protein folding studied by NMR. , 2004, Chemical reviews.

[79]  I. Kuntz,et al.  Hierarchical database screenings for HIV-1 reverse transcriptase using a pharmacophore model, rigid docking, solvation docking, and MM-PB/SA. , 2005, Journal of medicinal chemistry.

[80]  Rongda Xu,et al.  Automated high throughput ADME assays for metabolic stability and cytochrome P450 inhibition profiling of combinatorial libraries. , 2004, Journal of pharmaceutical and biomedical analysis.

[81]  G. Fasman.  Circular Dichroism and the Conformational Analysis of Biomolecules , 1996, Springer US.

[82]  T. Willson,et al.  The PPARs: From Orphan Receptors to Drug Discovery , 2000 .

[83]  E. Chien,et al.  Structure of a c-Kit Product Complex Reveals the Basis for Kinase Transactivation* , 2003, Journal of Biological Chemistry.

[84]  Thierry Langer,et al.  Impact of Scoring Functions on Enrichment in Docking-Based Virtual Screening: An Application Study on Renin Inhibitors , 2004, J. Chem. Inf. Model..

[85]  E. Mandelkow,et al.  Structural studies of tau protein and Alzheimer paired helical filaments show no evidence for beta-structure. , 1994, The Journal of biological chemistry.

[86]  Didier Rognan,et al.  Comparative evaluation of eight docking tools for docking and virtual screening accuracy , 2004, Proteins.

[87]  D. Rognan,et al.  Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. , 2000, Journal of medicinal chemistry.

[88]  O. Ptitsyn,et al.  Molten globule and protein folding. , 1995, Advances in protein chemistry.

[89]  Frank K. Pettit,et al.  Protein surface roughness and small molecular binding sites. , 1999, Journal of molecular biology.

[90]  Z. Obradovic,et al.  Identification and functions of usefully disordered proteins. , 2002, Advances in protein chemistry.

[91]  F. Cohen,et al.  An evolutionary trace method defines binding surfaces common to protein families. , 1996, Journal of molecular biology.

[92]  D. Shortle.  Structural analysis of non-native states of proteins by NMR methods. , 1996, Current opinion in structural biology.

[93]  I. Muegge.  Selection criteria for drug‐like compounds , 2003, Medicinal research reviews (Print).

[94]  D. Baker,et al.  A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[95]  Jonas Boström,et al.  Assessing the performance of OMEGA with respect to retrieving bioactive conformations. , 2003, Journal of molecular graphics & modelling.

[96]  H. Wolfson,et al.  Protein-Protein Interactions: Coupling of Structurally Conserved Residues and of Hot Spots across Interfaces. Implications for Docking , 2004 .

[97]  Christopher J. Oldfield,et al.  Intrinsic disorder in transcription factors. , 2006, Biochemistry.

[98]  R. Kiss,et al.  Calcium‐induced tripartite binding of intrinsically disordered calpastatin to its cognate enzyme, calpain , 2008, FEBS letters.

[99]  Thierry Langer,et al.  Recent Advances in Docking and Scoring , 2005 .

[100]  O. Ptitsyn,et al.  Further evidence on the equilibrium "pre-molten globule state": four-state guanidinium chloride-induced unfolding of carbonic anhydrase B at low temperature. , 1996, Journal of molecular biology.

[101]  O. F. Guener,et al.  An Integrated Approach to Three‐Dimensional Information Management with MACCS‐3D. , 1991 .

[102]  C. Chothia,et al.  Principles of protein–protein recognition , 1975, Nature.

[103]  Colin McMartin,et al.  QXP: Powerful, rapid computer algorithms for structure-based drug design , 1997, J. Comput. Aided Mol. Des..

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

[105]  Zhengyin Yan,et al.  Screening for reactive intermediates and toxicity assessment in drug discovery. , 2006, Current opinion in drug discovery & development.

[106]  Tudor I. Oprea,et al.  Property distribution of drug-related chemical databases* , 2000, J. Comput. Aided Mol. Des..

[107]  J. Beckmann,et al.  FoldIndex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded , 2005 .

[108]  Cyrus Chothia,et al.  The accessible surface area and stability of oligomeric proteins , 1987, Nature.

[109]  Wolfgang Sippl,et al.  Structure-based 3D QSAR and design of novel acetylcholinesterase inhibitors , 2001, J. Comput. Aided Mol. Des..

[110]  Tommi H. Nyrönen,et al.  A structure-activity relationship study of catechol-O-methyltransferase inhibitors combining molecular docking and 3D QSAR methods , 2003, J. Comput. Aided Mol. Des..

[111]  Jianzhi Zhang,et al.  Rapid Subfunctionalization Accompanied by Prolonged and Substantial Neofunctionalization in Duplicate Gene Evolution , 2005, Genetics.

[112]  Alan C. Cheng,et al.  Structure-Based Identification of Small Molecule Binding Sites Using a Free Energy Model , 2006, J. Chem. Inf. Model..

[113]  J. Berzofsky.  Intrinsic and extrinsic factors in protein antigenic structure. , 1985, Science.

[114]  Roland L. Dunbrack,et al.  Assessment of disorder predictions in CASP6 , 2005, Proteins.

[115]  Franco Lombardo,et al.  In silico ADME prediction: data, models, facts and myths. , 2003, Mini reviews in medicinal chemistry.

[116]  Z. Weng,et al.  Structure, function, and evolution of transient and obligate protein-protein interactions. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[117]  R Abagyan,et al.  Rapid boundary element solvation electrostatics calculations in folding simulations: successful folding of a 23-residue peptide. , 2001, Biopolymers.

[118]  Caleb J Bashor,et al.  The Ste5 Scaffold Allosterically Modulates Signaling Output of the Yeast Mating Pathway , 2006, Science.

[119]  J A McCammon,et al.  Accommodating protein flexibility in computational drug design. , 2000, Molecular pharmacology.

[120]  R. Laskowski.  SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. , 1995, Journal of molecular graphics.

[121]  Olivier Sperandio,et al.  MED-SuMoLig: A New Ligand-Based Screening Tool for Efficient Scaffold Hopping , 2007, J. Chem. Inf. Model..

[122]  H. Dyson,et al.  Intrinsically unstructured proteins and their functions , 2005, Nature Reviews Molecular Cell Biology.

[123]  D. Eisenberg,et al.  Detecting protein function and protein-protein interactions from genome sequences. , 1999, Science.

[124]  L. Patthy,et al.  Modules, multidomain proteins and organismic complexity , 2005, The FEBS journal.

[125]  M. Sternberg,et al.  The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. , 2005, Journal of molecular biology.

[126]  J. Bajorath.  Selected Concepts and Investigations in Compound Classification, Molecular Descriptor Analysis, and Virtual Screening , 2001 .

[127]  Elemer Mihalyi,et al.  Application of proteolytic enzymes to protein structure studies , 1972 .

[128]  K. Dill,et al.  Denatured states of proteins. , 1991, Annual review of biochemistry.

[129]  Roded Sharan,et al.  Comprehensive analysis of co-occurring domain sets in yeast proteins , 2007, BMC Genomics.

[130]  Heather A Carlson,et al.  Small molecule inhibitors of the MDM2-p53 interaction discovered by ensemble-based receptor models. , 2007, Journal of the American Chemical Society.

[131]  Nicola D. Gold,et al.  SitesBase: a database for structure-based protein–ligand binding site comparisons , 2005, Nucleic Acids Res..

[132]  R Nussinov,et al.  A proposed structural model for amyloid fibril elongation: domain swapping forms an interdigitating beta-structure polymer. , 2001, Protein engineering.

[133]  Jonathan M. Goodman,et al.  The ROBIA Program for Predicting Organic Reactivity , 2006, Journal of Chemical Information and Modeling.

[134]  T. Willson,et al.  Ligand binding and co-activator assembly of the peroxisome proliferator-activated receptor-γ , 1998, Nature.

[135]  Matthew Segall,et al.  In silico prediction of ADME properties: are we making progress? , 2004, Current opinion in drug discovery & development.

[136]  P. Hajduk,et al.  Druggability indices for protein targets derived from NMR-based screening data. , 2005, Journal of medicinal chemistry.

[137]  T. Clackson,et al.  A hot spot of binding energy in a hormone-receptor interface , 1995, Science.

[138]  G. Klebe,et al.  A new method to detect related function among proteins independent of sequence and fold homology. , 2002, Journal of molecular biology.

[139]  Karen N. Allen,et al.  An Experimental Approach to Mapping the Binding Surfaces of Crystalline Proteins , 1996 .

[140]  Tal Pupko,et al.  In silico identification of functional regions in proteins , 2005, ISMB.

[141]  Robert B. Russell,et al.  DILIMOT: discovery of linear motifs in proteins , 2006, Nucleic Acids Res..

[142]  Jill E. Gready,et al.  Identification and energetic ranking of possible docking sites for pterin on dihydrofolate reductase , 1998, J. Comput. Aided Mol. Des..

[143]  B. Shoichet,et al.  Soft docking and multiple receptor conformations in virtual screening. , 2004, Journal of medicinal chemistry.

[144]  Stephen H. Bryant,et al.  Domain size distributions can predict domain boundaries , 2000, Bioinform..

[145]  B. Pontius.  Close encounters: why unstructured, polymeric domains can increase rates of specific macromolecular association. , 1993, Trends in biochemical sciences.

[146]  M F Lensink,et al.  Recognition-induced conformational changes in protein-protein docking. , 2008, Current pharmaceutical biotechnology.

[147]  Zsolt Zsoldos,et al.  LASSO—ligand activity by surface similarity order: a new tool for ligand based virtual screening , 2008, J. Comput. Aided Mol. Des..

[148]  G. Petsko,et al.  Multiple solvent crystal structures: probing binding sites, plasticity and hydration. , 2006, Journal of molecular biology.

[149]  Marc S. Cortese,et al.  Flexible nets , 2005, The FEBS journal.

[150]  D. Moore,et al.  Dynamic stabilization of nuclear receptor ligand binding domains by hormone or corepressor binding. , 2000, Molecular cell.

[151]  Humberto González Díaz,et al.  Simple stochastic fingerprints towards mathematical modelling in biology and medicine. 1. The treatment of coccidiosis , 2004, Bulletin of mathematical biology.

[152]  M. Sternberg,et al.  Prediction of protein-protein interactions by docking methods. , 2002, Current opinion in structural biology.

[153]  B. Shoichet,et al.  A specific mechanism of nonspecific inhibition. , 2003, Journal of medicinal chemistry.

[154]  Li Xing,et al.  Evaluation and application of multiple scoring functions for a virtual screening experiment , 2004, J. Comput. Aided Mol. Des..

[155]  S. Fletcher,et al.  Targeting protein–protein interactions by rational design: mimicry of protein surfaces , 2006, Journal of The Royal Society Interface.

[156]  A J Olson,et al.  Morphology of protein-protein interfaces. , 1998, Structure.

[157]  Ruben Abagyan,et al.  Four-dimensional docking: a fast and accurate account of discrete receptor flexibility in ligand docking. , 2009, Journal of medicinal chemistry.

[158]  P. Tompa.  Intrinsically unstructured proteins evolve by repeat expansion , 2003, BioEssays : news and reviews in molecular, cellular and developmental biology.

[159]  Didier Rognan,et al.  Assessing the Scaffold Diversity of Screening Libraries , 2006, J. Chem. Inf. Model..

[160]  Patrick Aloy,et al.  Interrogating protein interaction networks through structural biology , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[161]  Magdalena Bacilieri,et al.  Autocorrelation of molecular electrostatic potential surface properties combined with partial least squares analysis as alternative attractive tool to generate ligand-based 3D-QSARs. , 2005, Current drug discovery technologies.

[162]  P. Kollman,et al.  Computational Alanine Scanning To Probe Protein−Protein Interactions: A Novel Approach To Evaluate Binding Free Energies , 1999 .

[163]  Renxiao Wang,et al.  Comparative evaluation of 11 scoring functions for molecular docking. , 2003, Journal of medicinal chemistry.

[164]  Zsuzsanna Dosztányi,et al.  IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content , 2005, Bioinform..

[165]  Ozlem Keskin,et al.  Characterization and prediction of protein interfaces to infer protein-protein interaction networks. , 2008, Current pharmaceutical biotechnology.

[166]  Sonia Longhi,et al.  A practical overview of protein disorder prediction methods , 2006, Proteins.

[167]  Ruben Abagyan,et al.  New Method for the Assessment of All Drug-Like Pockets Across a Structural Genome , 2008, J. Comput. Biol..

[168]  L. Aravind,et al.  The many faces of the helix-turn-helix domain: transcription regulation and beyond. , 2005, FEMS microbiology reviews.

[169]  Ting Wang,et al.  Protein–protein docking by simulating the process of association subject to biochemical constraints , 2008, Proteins.

[170]  Mika A. Kastenholz,et al.  GRID/CPCA: a new computational tool to design selective ligands. , 2000, Journal of medicinal chemistry.

[171]  A Keith Dunker,et al.  Natively Disordered Proteins , 2004, Applied bioinformatics.

[172]  H. Wolfson,et al.  A new, structurally nonredundant, diverse data set of protein–protein interfaces and its implications , 2004, Protein science : a publication of the Protein Society.

[173]  Christopher J. Oldfield,et al.  Intrinsically disordered protein. , 2001, Journal of molecular graphics & modelling.

[174]  Bruce Tidor,et al.  Optimal charges in lead progression: a structure-based neuraminidase case study. , 2006, Journal of medicinal chemistry.

[175]  R. Nussinov,et al.  Protein–protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach , 2005, Physical biology.

[176]  R Abagyan,et al.  High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.

[177]  B. Rost,et al.  Analysing six types of protein-protein interfaces. , 2003, Journal of molecular biology.

[178]  O. Keskina,et al.  Towards Drugs Targeting Multiple Proteins in a Systems Biology Approach , 2008 .

[179]  A. Elofsson,et al.  Quantification of the elevated rate of domain rearrangements in metazoa. , 2007, Journal of molecular biology.

[180]  M. Vasák,et al.  Solution structure of native proteins with irregular folds from Raman optical activity. , 2001, Biopolymers.

[181]  V. De Filippis,et al.  Probing the conformational state of apomyoglobin by limited proteolysis. , 1997, Journal of molecular biology.

[182]  J. Lehmann,et al.  A peroxisome proliferator-activated receptor gamma ligand inhibits adipocyte differentiation. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[183]  C. DeLisi,et al.  Genes linked by fusion events are generally of the same functional category: A systematic analysis of 30 microbial genomes , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[184]  H. Carlson.  Protein flexibility and drug design: how to hit a moving target. , 2002, Current opinion in chemical biology.

[185]  Z. Weng,et al.  Protein–protein docking benchmark version 3.0 , 2008, Proteins.

[186]  Sandor Vajda,et al.  Algorithms for computational solvent mapping of proteins , 2003, Proteins.

[187]  Arne Elofsson,et al.  A comparison of sequence and structure protein domain families as a basis for structural genomics , 1999, Bioinform..

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

[189]  Tanja Kortemme,et al.  Computational design of protein-protein interactions. , 2004, Current opinion in chemical biology.

[190]  B. Matthews,et al.  Structural basis for the action of thermolysin. , 1992, Matrix (Stuttgart, Germany). Supplement.

[191]  R. Nolen.  'Between a rock and a hard place'. , 2002, Journal of the American Veterinary Medical Association.

[192]  A. Li,et al.  Screening for human ADME/Tox drug properties in drug discovery. , 2001, Drug discovery today.

[193]  Hongwei Wu,et al.  Solution structure of a dynein motor domain associated light chain , 2000, Nature Structural Biology.

[194]  Hongyu Zhao,et al.  Scaffold selection and scaffold hopping in lead generation: a medicinal chemistry perspective. , 2007, Drug discovery today.

[195]  R. Abagyan,et al.  Optimal docking area: A new method for predicting protein–protein interaction sites , 2004, Proteins.

[196]  Cyrus Chothia,et al.  Protein Family Expansions and Biological Complexity , 2006, PLoS Comput. Biol..

[197]  D. Labuda,et al.  Alu sequences in the coding regions of mRNA: a source of protein variability. , 1994, Trends in genetics : TIG.

[198]  M. Cox,et al.  RecA protein: structure, function, and role in recombinational DNA repair. , 1997, Progress in nucleic acid research and molecular biology.

[199]  Robert P Sheridan,et al.  Why do we need so many chemical similarity search methods? , 2002, Drug discovery today.

[200]  Maria A Miteva,et al.  Structure‐based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections , 2007, Proteins.

[201]  Ruth Nussinov,et al.  Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers. , 2004, Journal of molecular biology.

[202]  D. Frank Hsu,et al.  Consensus Scoring Criteria for Improving Enrichment in Virtual Screening , 2005, J. Chem. Inf. Model..

[203]  H. Wolfson,et al.  Shape complementarity at protein–protein interfaces , 1994, Biopolymers.

[204]  D. Shortle,et al.  Residual helical and turn structure in the denatured state of staphylococcal nuclease: analysis of peptide fragments. , 1997, Folding & design.

[205]  R. Marmorstein,et al.  Molecular basis for Gcn5/PCAF histone acetyltransferase selectivity for histone and nonhistone substrates. , 2003, Biochemistry.

[206]  L Xue,et al.  Molecular descriptors in chemoinformatics, computational combinatorial chemistry, and virtual screening. , 2000, Combinatorial chemistry & high throughput screening.

[207]  H. Edelsbrunner,et al.  Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design , 1998, Protein science : a publication of the Protein Society.

[208]  Adam Godzik,et al.  Comparative analysis of protein domain organization. , 2004, Genome research.

[209]  Ruben Abagyan,et al.  Prediction of the binding energy for small molecules, peptides and proteins , 1999, Journal of molecular recognition : JMR.

[210]  Ilya A Vakser,et al.  Predicting 3D structures of protein-protein complexes. , 2008, Current pharmaceutical biotechnology.

[211]  István Simon,et al.  Molecular principles of the interactions of disordered proteins. , 2007, Journal of molecular biology.

[212]  L. Patthy.  Modular Assembly of Genes and the Evolution of New Functions , 2003, Genetica.

[213]  Ruth Nussinov,et al.  Principles of docking: An overview of search algorithms and a guide to scoring functions , 2002, Proteins.

[214]  B. Kuhn,et al.  Validation and use of the MM-PBSA approach for drug discovery. , 2005, Journal of medicinal chemistry.

[215]  J. Bajorath,et al.  Mini-fingerprints for virtual screening: Design principles and generation of novel prototypes based on information theory , 2003, SAR and QSAR in environmental research.

[216]  P. Romero,et al.  Sequence complexity of disordered protein , 2001, Proteins.

[217]  Petra Schneider,et al.  Comparison of correlation vector methods for ligand-based similarity searching , 2003, J. Comput. Aided Mol. Des..

[218]  Heather A Carlson,et al.  Protein flexibility and species specificity in structure-based drug discovery: dihydrofolate reductase as a test system. , 2007, Journal of the American Chemical Society.

[219]  Leslie A. Kuhn,et al.  Database Screening for HIV Protease Ligands: The Influence of Binding-Site Conformation and Representation on Ligand Selectivity , 1999, ISMB.

[220]  Pieter F. W. Stouten,et al.  Fast prediction and visualization of protein binding pockets with PASS , 2000, J. Comput. Aided Mol. Des..

[221]  N. Ben-Tal,et al.  The ConSurf‐HSSP database: The mapping of evolutionary conservation among homologs onto PDB structures , 2004, Proteins.

[222]  N. Gray,et al.  Rational design of inhibitors that bind to inactive kinase conformations , 2006, Nature chemical biology.

[223]  Martin Zacharias,et al.  Rapid protein–ligand docking using soft modes from molecular dynamics simulations to account for protein deformability: Binding of FK506 to FKBP , 2004, Proteins.

[224]  Shoshana J. Wodak,et al.  LigASite—a database of biologically relevant binding sites in proteins with known apo-structures , 2007, Nucleic Acids Res..

[225]  Joshua N Adkins,et al.  Functional consequences of preorganized helical structure in the intrinsically disordered cell-cycle inhibitor p27(Kip1). , 2001, Biochemistry.

[226]  C. Bell,et al.  Crystal structures of Escherichia coli RecA in complex with MgADP and MnAMP-PNP. , 2004, Biochemistry.

[227]  David W. Ritchie,et al.  Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions , 2008, Bioinform..

[228]  E. Eichler,et al.  Recent duplication, domain accretion and the dynamic mutation of the human genome. , 2001, Trends in genetics : TIG.

[229]  Y. Martin,et al.  A bioavailability score. , 2005, Journal of medicinal chemistry.

[230]  Gennady M Verkhivker,et al.  Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming. , 1995, Chemistry & biology.

[231]  Michelle Arkin,et al.  Protein-protein interactions and cancer: small molecules going in for the kill. , 2005, Current opinion in chemical biology.

[232]  M. Grütter,et al.  The crystal structures of recombinant glycosylated human renin alone and in complex with a transition state analog inhibitor. , 1991, Journal of structural biology.

[233]  Anton J. Enright,et al.  Protein interaction maps for complete genomes based on gene fusion events , 1999, Nature.

[234]  Brian W. Matthews,et al.  Structural basis of the action of thermolysin and related zinc peptidases , 1988 .

[235]  P. N. Lewis,et al.  Unstructured Conformations Are a Substrate Requirement for the Sir2 Family of NAD-dependent Protein Deacetylases* , 2005, Journal of Biological Chemistry.

[236]  Ruben Abagyan,et al.  A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE) , 2008, J. Comput. Aided Mol. Des..

[237]  P E Wright,et al.  Conformational preferences in the Ser133‐phosphorylated and non‐phosphorylated forms of the kinase inducible transactivation domain of CREB , 1998, FEBS letters.

[238]  J. S. Sodhi,et al.  Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. , 2004, Journal of molecular biology.

[239]  L. Patthy.  Modular design of proteases of coagulation, fibrinolysis, and complement activation: implications for protein engineering and structure-function studies. , 1993, Methods in enzymology.

[240]  Thierry Heidmann,et al.  Human LINE retrotransposons generate processed pseudogenes , 2000, Nature Genetics.

[241]  Heather A Carlson,et al.  Protein flexibility is an important component of structure-based drug discovery. , 2002, Current pharmaceutical design.

[242]  Sandor Vajda,et al.  Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. , 2007, Journal of medicinal chemistry.

[243]  P. Lansbury,et al.  NACP, a protein implicated in Alzheimer's disease and learning, is natively unfolded. , 1996, Biochemistry.

[244]  Anna Lorenc,et al.  Transposable Elements and Vertebrate Protein Diversity , 2003, Genetica.

[245]  J. Schwabe,et al.  A dynamic mechanism of nuclear receptor activation and its perturbation in a human disease , 2003, Nature Structural Biology.

[246]  Kurt S. Thorn,et al.  ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions , 2001, Bioinform..

[247]  A Keith Dunker,et al.  Intrinsic disorder in pathogenic and non-pathogenic microbes: discovering and analyzing the unfoldomes of early-branching eukaryotes. , 2008, Molecular bioSystems.

[248]  Dominique Douguet,et al.  DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking , 2007, Proteins.

[249]  Daniel R. Caffrey,et al.  Are protein–protein interfaces more conserved in sequence than the rest of the protein surface? , 2004, Protein science : a publication of the Protein Society.

[250]  E Lucile White,et al.  Development and Validation of a High-Throughput Screen for Inhibitors of SARS CoV and Its Application in Screening of a 100,000-Compound Library , 2007, SLAS Discovery.

[251]  Jin Li,et al.  On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors , 2006, J. Chem. Inf. Model..

[252]  H A Scheraga,et al.  Reaching the global minimum in docking simulations: a Monte Carlo energy minimization approach using Bezier splines. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[253]  L. Vassilev,et al.  In Vivo Activation of the p53 Pathway by Small-Molecule Antagonists of MDM2 , 2004, Science.

[254]  Vladimir N Uversky,et al.  Neuropathology, biochemistry, and biophysics of alpha-synuclein aggregation. , 2007, Journal of neurochemistry.

[255]  C. Venkatachalam,et al.  LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. , 2003, Journal of molecular graphics & modelling.

[256]  Atanas V Koulov,et al.  Functional amyloid--from bacteria to humans. , 2007, Trends in biochemical sciences.

[257]  N. Pavletich,et al.  Structure of the p53 Tumor Suppressor Bound to the Ankyrin and SH3 Domains of 53BP2 , 1996, Science.

[258]  R E Hubbard,et al.  Experimental and computational mapping of the binding surface of a crystalline protein. , 2001, Protein engineering.

[259]  C. Venkatachalam,et al.  LigScore: a novel scoring function for predicting binding affinities. , 2005, Journal of molecular graphics & modelling.

[260]  N. Blomberg,et al.  Structure of the PPARalpha and -gamma ligand binding domain in complex with AZ 242; ligand selectivity and agonist activation in the PPAR family. , 2001, Structure.

[261]  L. Pearl,et al.  Structural basis for recruitment of glycogen synthase kinase 3β to the axin—APC scaffold complex , 2003, The EMBO journal.

[262]  Sarah A Teichmann,et al.  Relative rates of gene fusion and fission in multi-domain proteins. , 2005, Trends in genetics : TIG.

[263]  Krzysztof Fidelis,et al.  Progress from CASP6 to CASP7 , 2007, Proteins.

[264]  Vladimir N Uversky,et al.  A Protein-Chameleon: Conformational Plasticity of α-Synuclein, a Disordered Protein Involved in Neurodegenerative Disorders , 2003, Journal of biomolecular structure & dynamics.

[265]  W Patrick Walters,et al.  A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance , 2004, Proteins.

[266]  J. Sturis,et al.  Novel tricyclic-alpha-alkyloxyphenylpropionic acids: dual PPARalpha/gamma agonists with hypolipidemic and antidiabetic activity. , 2002, Journal of medicinal chemistry.

[267]  Wolfgang Guba,et al.  Recent developments in de novo design and scaffold hopping. , 2008, Current opinion in drug discovery & development.

[268]  R. Abagyan,et al.  Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. , 1994, Journal of molecular biology.

[269]  Ruben Abagyan,et al.  REVCOM: a robust Bayesian method for evolutionary rate estimation , 2005, Bioinform..

[270]  A Keith Dunker,et al.  Protein intrinsic disorder and human papillomaviruses: increased amount of disorder in E6 and E7 oncoproteins from high risk HPVs. , 2006, Journal of proteome research.

[271]  Jeffrey J. Gray,et al.  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. , 2003, Journal of molecular biology.

[272]  J. Bajorath,et al.  Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.

[273]  Barry Honig,et al.  On the role of electrostatic interactions in the design of protein-protein interfaces. , 2002, Journal of molecular biology.

[274]  L. Jendeberg,et al.  Crystal Structure of the Ligand Binding Domain of the Human Nuclear Receptor PPARγ* , 1998, The Journal of Biological Chemistry.

[275]  Petra Schneider,et al.  Scaffold Hopping by “Fuzzy” Pharmacophores and its Application to RNA Targets , 2007, Chembiochem : a European journal of chemical biology.

[276]  M. Murcko,et al.  Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. , 1999, Journal of medicinal chemistry.

[277]  Obradovic,et al.  Predicting Binding Regions within Disordered Proteins. , 1999, Genome informatics. Workshop on Genome Informatics.

[278]  A. Elofsson,et al.  Domain rearrangements in protein evolution. , 2005, Journal of molecular biology.

[279]  C Chothia,et al.  Surface, subunit interfaces and interior of oligomeric proteins. , 1988, Journal of molecular biology.

[280]  R E Hubbard,et al.  Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol , 1999, Proteins.

[281]  D. Shortle.  The denatured state (the other half of the folding equation) and its role in protein stability , 1996, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[282]  A. Good,et al.  3-D pharmacophores in drug discovery. , 2001, Current pharmaceutical design.

[283]  Mary P. Bradley.  An overview of the diversity represented in commercially-available databases , 2002, J. Comput. Aided Mol. Des..

[284]  Rebecca C Wade,et al.  Biomolecular diffusional association. , 2002, Current opinion in structural biology.

[285]  Kaushik Dutta,et al.  The regions of securin and cyclin B proteins recognized by the ubiquitination machinery are natively unfolded , 2002, FEBS letters.

[286]  Shaomeng Wang,et al.  MCDOCK: A Monte Carlo simulation approach to the molecular docking problem , 1999, J. Comput. Aided Mol. Des..

[287]  George Karypis,et al.  Method for effective virtual screening and scaffold-hopping in chemical compounds. , 2007, Computational systems bioinformatics. Computational Systems Bioinformatics Conference.

[288]  Thierry Langer,et al.  Fast and Efficient in Silico 3D Screening: Toward Maximum Computational Efficiency of Pharmacophore-Based and Shape-Based Approaches , 2007, J. Chem. Inf. Model..

[289]  D. Kassel,et al.  Applications of high-throughput ADME in drug discovery. , 2004, Current opinion in chemical biology.

[290]  Georg E. Schulz,et al.  Nucleotide binding proteins , 1979 .

[291]  J. Berger,et al.  The mechanisms of action of PPARs. , 2002, Annual review of medicine.

[292]  A Keith Dunker,et al.  Combining prediction, computation and experiment for the characterization of protein disorder. , 2004, Current opinion in structural biology.

[293]  Volkhard Helms,et al.  Protein dynamics tightly connected to the dynamics of surrounding and internal water molecules. , 2007, Chemphyschem : a European journal of chemical physics and physical chemistry.

[294]  Encoding Rules,et al.  SMILES, a Chemical Language and Information System. 1. Introduction to Methodology , 1988 .

[295]  Jens Meiler,et al.  ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility , 2006, Proteins.

[296]  J. Thornton,et al.  A method for localizing ligand binding pockets in protein structures , 2005, Proteins.

[297]  Stephen R. Comeau,et al.  PIPER: An FFT‐based protein docking program with pairwise potentials , 2006, Proteins.

[298]  J M Blaney,et al.  A geometric approach to macromolecule-ligand interactions. , 1982, Journal of molecular biology.

[299]  P. Tompa.  The interplay between structure and function in intrinsically unstructured proteins , 2005, FEBS letters.

[300]  Alexander Heifetz,et al.  Protein–protein docking: Progress in CAPRI rounds 6–12 using a combination of methods: The introduction of steered solvated molecular dynamics , 2007, Proteins.

[301]  R. Fåhraeus,et al.  In silico-in vitro screening of protein-protein interactions: towards the next generation of therapeutics. , 2008, Current pharmaceutical biotechnology.

[302]  B. Matthews,et al.  A model binding site for testing scoring functions in molecular docking. , 2002, Journal of molecular biology.

[303]  O. Ptitsyn.  Kinetic and equilibrium intermediates in protein folding. , 1994, Protein engineering.

[304]  J. Janin,et al.  A dissection of specific and non-specific protein-protein interfaces. , 2004, Journal of molecular biology.

[305]  Stephen R. Johnson,et al.  Molecular properties that influence the oral bioavailability of drug candidates. , 2002, Journal of medicinal chemistry.

[306]  Ozlem Keskin,et al.  Similar binding sites and different partners: implications to shared proteins in cellular pathways. , 2007, Structure.

[307]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[308]  Ajay N. Jain.  Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. , 2003, Journal of medicinal chemistry.

[309]  Robert P. Sheridan,et al.  FLOG: A system to select ‘quasi-flexible’ ligands complementary to a receptor of known three-dimensional structure , 1994, J. Comput. Aided Mol. Des..

[310]  Michelle R. Arkin,et al.  Small-molecule inhibitors of protein–protein interactions: progressing towards the dream , 2004, Nature Reviews Drug Discovery.

[311]  N. Ben-Tal,et al.  ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. , 2001, Journal of molecular biology.

[312]  D. Eliezer,et al.  Residual Structure and Dynamics in Parkinson's Disease-associated Mutants of α-Synuclein* , 2001, The Journal of Biological Chemistry.

[313]  D. Shortle,et al.  Characterization of long-range structure in the denatured state of staphylococcal nuclease. II. Distance restraints from paramagnetic relaxation and calculation of an ensemble of structures. , 1997, Journal of molecular biology.

[314]  T L Blundell,et al.  Domain flexibility in aspartic proteinases , 1992, Proteins.

[315]  István Simon,et al.  BIOINFORMATICS ORIGINAL PAPER doi:10.1093/bioinformatics/btm035 Structural bioinformatics Local structural disorder imparts plasticity on linear motifs , 2022 .

[316]  David T. Jones,et al.  Prediction of disordered regions in proteins from position specific score matrices , 2003, Proteins.

[317]  Ruben Abagyan,et al.  PIER: Protein interface recognition for structural proteomics , 2007, Proteins.

[318]  Yong-Jun Jiang,et al.  Three-dimensional QSAR of HPPD inhibitors, PSA inhibitors, and anxiolytic agents: effect of tautomerism on the CoMFA models. , 2007, Journal of molecular graphics & modelling.

[319]  G. Wagner,et al.  The interaction of eIF4E with 4E‐BP1 is an induced fit to a completely disordered protein , 1998, Protein science : a publication of the Protein Society.

[320]  Thomas Stützle,et al.  PLANTS: Application of Ant Colony Optimization to Structure-Based Drug Design , 2006, ANTS Workshop.

[321]  Sandor Vajda,et al.  Computational mapping identifies the binding sites of organic solvents on proteins , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[322]  Andrew R. Leach,et al.  A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP , 2002, J. Comput. Aided Mol. Des..

[323]  Torsten Schwede,et al.  Assessment of disorder predictions in CASP7 , 2007, Proteins.

[324]  Evidence by site-directed mutagenesis that arginine 203 of thermolysin and arginine 717 of neprilysin (neutral endopeptidase) play equivalent critical roles in substrate hydrolysis and inhibitor binding. , 1997, Biochemistry.

[325]  Barry Honig,et al.  Sequence and structural determinants of strand swapping in cadherin domains: do all cadherins bind through the same adhesive interface? , 2008, Journal of molecular biology.

[326]  Bernard F. Buxton,et al.  The DISOPRED server for the prediction of protein disorder , 2004, Bioinform..

[327]  R. Bruccoleri,et al.  On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. , 1989, Biochemistry.

[328]  John H. Van Drie,et al.  Pharmacophore Discovery - Lessons Learned , 2003 .

[329]  Wolfgang Sippl,et al.  Development of biologically active compounds by combining 3D QSAR and structure-based design methods , 2002, J. Comput. Aided Mol. Des..

[330]  V. Uversky,et al.  A multiparametric approach to studies of self-organization of globular proteins , 1999, Biochemistry. Biokhimiia.

[331]  Zoran Obradovic,et al.  Length-dependent prediction of protein intrinsic disorder , 2006, BMC Bioinformatics.

[332]  E. Koonin,et al.  The structure of the protein universe and genome evolution , 2002, Nature.

[333]  A. Dunker,et al.  Disorder and sequence repeats in hub proteins and their implications for network evolution. , 2006, Journal of proteome research.

[334]  Andrew J. Martin,et al.  Antibody-antigen interactions: contact analysis and binding site topography. , 1996, Journal of molecular biology.

[335]  Alasdair T. R. Laurie,et al.  Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. , 2006, Current protein & peptide science.

[336]  D. Shortle,et al.  Characterization of long-range structure in the denatured state of staphylococcal nuclease. I. Paramagnetic relaxation enhancement by nitroxide spin labels. , 1997, Journal of molecular biology.

[337]  A. Bogan,et al.  Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.

[338]  G. Marius Clore,et al.  Improving the Packing and Accuracy of NMR Structures with a Pseudopotential for the Radius of Gyration , 1999 .

[339]  Olivier Sperandio,et al.  Free resources to assist structure-based virtual ligand screening experiments. , 2007, Current protein & peptide science.

[340]  J Andrew McCammon,et al.  Molecular docking of balanol to dynamics snapshots of protein kinase A , 2005, Proteins.

[341]  Christopher L. McClendon,et al.  Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.

[342]  Christophe Combet,et al.  The SuMo server: 3D search for protein functional sites , 2005, Bioinform..

[343]  C. Chothia,et al.  The atomic structure of protein-protein recognition sites. , 1999, Journal of molecular biology.

[344]  Christopher W. V. Hogue,et al.  Analysis of domain correlations in yeast protein complexes , 2004, ISMB/ECCB.

[345]  David W Ritchie,et al.  Recent progress and future directions in protein-protein docking. , 2008, Current protein & peptide science.

[346]  L. Amos,et al.  Molecules of the bacterial cytoskeleton. , 2004, Annual review of biophysics and biomolecular structure.

[347]  R. Srinivasan,et al.  The Flory isolated-pair hypothesis is not valid for polypeptide chains: implications for protein folding. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[348]  S. Teichmann,et al.  Domain combinations in archaeal, eubacterial and eukaryotic proteomes. , 2001, Journal of molecular biology.

[349]  N. Sonenberg,et al.  The translation initiation factor eIF-4E binds to a common motif shared by the translation factor eIF-4 gamma and the translational repressors 4E-binding proteins , 1995, Molecular and cellular biology.

[350]  P. Hajduk,et al.  Predicting protein druggability. , 2005, Drug discovery today.

[351]  Ivo Tews,et al.  Specificity determinants of recruitment peptides bound to phospho-CDK2/cyclin A. , 2002, Biochemistry.

[352]  J. Janin,et al.  Dissecting protein–protein recognition sites , 2002, Proteins.

[353]  Maria A Miteva,et al.  Fast structure-based virtual ligand screening combining FRED, DOCK, and Surflex. , 2005, Journal of medicinal chemistry.

[354]  N. Paul,et al.  Recovering the true targets of specific ligands by virtual screening of the protein data bank , 2004, Proteins.

[355]  Steven Fletcher,et al.  Protein-protein interaction inhibitors: small molecules from screening techniques. , 2007, Current topics in medicinal chemistry.

[356]  Andreas Vitalis,et al.  Quantitative characterization of intrinsic disorder in polyglutamine: insights from analysis based on polymer theories. , 2007, Biophysical journal.

[357]  B. Shoichet,et al.  Probing molecular docking in a charged model binding site. , 2006, Journal of molecular biology.

[358]  Paul Labute,et al.  Derivation and applications of molecular descriptors based on approximate surface area. , 2004, Methods in molecular biology.

[359]  Zohar Itzhaki,et al.  Evolutionary conservation of domain-domain interactions , 2006, Genome Biology.

[360]  S. Taylor,et al.  Two well‐defined motifs in the cAMP‐dependent protein kinase inhibitor (PKIα) correlate with inhibitory and nuclear export function , 2008, Protein science : a publication of the Protein Society.

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

[362]  P. Seeburg,et al.  Structural mechanism for STI-571 inhibition of abelson tyrosine kinase. , 2000, Science.

[363]  M. Suyama,et al.  Complex genomic rearrangements lead to novel primate gene function. , 2005, Genome research.

[364]  Vijay K Gombar,et al.  Predicting P-glycoprotein substrates by a quantitative structure-activity relationship model. , 2004, Journal of pharmaceutical sciences.

[365]  R. Abagyan,et al.  Flexible ligand docking to multiple receptor conformations: a practical alternative. , 2008, Current opinion in structural biology.

[366]  Vladimir N Uversky,et al.  What does it mean to be natively unfolded? , 2002, European journal of biochemistry.

[367]  Christopher J. Oldfield,et al.  Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners , 2008, BMC Genomics.

[368]  D S Goodsell,et al.  Automated docking of flexible ligands: Applications of autodock , 1996, Journal of molecular recognition : JMR.

[369]  S. Olson,et al.  Role of the antithrombin-binding pentasaccharide in heparin acceleration of antithrombin-proteinase reactions. Resolution of the antithrombin conformational change contribution to heparin rate enhancement. , 1992, The Journal of biological chemistry.

[370]  Brian K Shoichet,et al.  Testing a flexible-receptor docking algorithm in a model binding site. , 2004, Journal of molecular biology.

[371]  Thomas Bäck,et al.  Mining a Chemical Database for Fragment Co-occurrence: Discovery of "Chemical Clichés" , 2006, J. Chem. Inf. Model..

[372]  S. Wodak,et al.  Assessment of blind predictions of protein–protein interactions: Current status of docking methods , 2003, Proteins.

[373]  I. Kuntz,et al.  Inclusion of Solvation in Ligand Binding Free Energy Calculations Using the Generalized-Born Model , 1999 .

[374]  J. Thornton,et al.  Protein–protein interfaces: Analysis of amino acid conservation in homodimers , 2001, Proteins.

[375]  Peter Tompa,et al.  Primary contact sites in intrinsically unstructured proteins: the case of calpastatin and microtubule-associated protein 2. , 2005, Biochemistry.

[376]  P. Stogios,et al.  Sequence and structural analysis of BTB domain proteins , 2005, Genome Biology.

[377]  A. Iglesias,et al.  Intrinsic disorder is a key characteristic in partners that bind 14‐3‐3 proteins , 2006, Proteins.

[378]  J. Thornton,et al.  Structural characterisation and functional significance of transient protein-protein interactions. , 2003, Journal of molecular biology.

[379]  M. Schroeder,et al.  LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation , 2006, BMC Structural Biology.

[380]  J. Wood,et al.  Structure-based drug design: the discovery of novel nonpeptide orally active inhibitors of human renin. , 2000, Chemistry & biology.

[381]  S. Teague.  Implications of protein flexibility for drug discovery , 2003, Nature Reviews Drug Discovery.

[382]  Veerabahu Shanmugasundaram,et al.  Estimation of Aqueous Solubility of Organic Compounds with QSPR Approach , 2002, Pharmaceutical Research.

[383]  P Argos,et al.  A method to configure protein side-chains from the main-chain trace in homology modelling. , 1993, Journal of molecular biology.

[384]  D. Eliezer,et al.  Residual structure, backbone dynamics, and interactions within the synuclein family. , 2007, Journal of molecular biology.

[385]  Eugene V Koonin,et al.  Comparative genomics and structural biology of the molecular innovations of eukaryotes. , 2006, Current opinion in structural biology.

[386]  R. Abagyan,et al.  Pocketome via Comprehensive Identification and Classification of Ligand Binding Envelopes* , 2005, Molecular & Cellular Proteomics.

[387]  Tudor I. Oprea.  Current trends in lead discovery: Are we looking for the appropriate properties? , 2002, J. Comput. Aided Mol. Des..

[388]  R Abagyan,et al.  Flexible protein–ligand docking by global energy optimization in internal coordinates , 1997, Proteins.

[389]  Wen-Hsiung Li,et al.  Fundamentals of molecular evolution , 1990 .

[390]  H. Dyson,et al.  Insights into the structure and dynamics of unfolded proteins from nuclear magnetic resonance. , 2002, Advances in protein chemistry.

[391]  Jong H. Park,et al.  Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. , 2001, Journal of molecular biology.

[392]  H. Wolfson,et al.  Recognition of Functional Sites in Protein Structures☆ , 2004, Journal of Molecular Biology.

[393]  A. Weiner,et al.  Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. , 1986, Annual review of biochemistry.

[394]  Thomas Lengauer,et al.  Time-Efficient Docking of Flexible Ligands into Active Sites of Proteins , 1995, ISMB.

[395]  A. Nassar,et al.  Strategies for dealing with reactive intermediates in drug discovery and development. , 2004, Current opinion in drug discovery & development.

[396]  Siegfried Labeit,et al.  Titin Extensibility In Situ: Entropic Elasticity of Permanently Folded and Permanently Unfolded Molecular Segments , 1998, The Journal of cell biology.

[397]  Wolfgang Sippl,et al.  Receptor-based 3D QSAR analysis of estrogen receptor ligands – merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods , 2000, J. Comput. Aided Mol. Des..

[398]  K. Knight,et al.  Functionally important residues at a subunit interface site in the RecA protein from Escherichia coli. , 1994, The Journal of biological chemistry.

[399]  David R Westhead,et al.  Asymmetric mutation rates at enzyme–inhibitor interfaces: Implications for the protein–protein docking problem , 2003, Protein science : a publication of the Protein Society.

[400]  Claudio N. Cavasotto,et al.  Representing receptor flexibility in ligand docking through relevant normal modes. , 2005, Journal of the American Chemical Society.

[401]  B. Kowalski,et al.  Partial least-squares regression: a tutorial , 1986 .

[402]  J. Peters,et al.  Regulation of Human Separase by Securin Binding and Autocleavage , 2002, Current Biology.

[403]  R. Hartmann,et al.  Prediction of protein-protein interaction inhibitors by chemoinformatics and machine learning methods. , 2007, Journal of medicinal chemistry.

[404]  Timothy Clark,et al.  ParaFrag—an approach for surface-based similarity comparison of molecular fragments , 2008, Journal of molecular modeling.

[405]  P E Wright,et al.  Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk2-bound state: conformational disorder mediates binding diversity. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[406]  D. Ringe,et al.  Proteins in organic solvents. , 2001, Current opinion in structural biology.

[407]  Huan-Xiang Zhou,et al.  A holistic approach to protein docking , 2007, Proteins.

[408]  Johann Gasteiger.  Physicochemical effects in the representation of molecular structures for drug designing. , 2003, Mini reviews in medicinal chemistry.

[409]  Dima Kozakov,et al.  Fragment-based identification of druggable 'hot spots' of proteins using Fourier domain correlation techniques , 2009, Bioinform..

[410]  S. Gellman,et al.  Targeting protein-protein interactions: lessons from p53/MDM2. , 2007, Biopolymers.

[411]  P Argos,et al.  Hydrophobic patches on protein subunit interfaces: Characteristics and prediction , 1997, Proteins.

[412]  T. Pawson,et al.  Signaling through scaffold, anchoring, and adaptor proteins. , 1997, Science.

[413]  T. Pawson,et al.  Assembly of Cell Regulatory Systems Through Protein Interaction Domains , 2003, Science.

[414]  R. Nussinov,et al.  Protein–protein interactions: Structurally conserved residues distinguish between binding sites and exposed protein surfaces , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[415]  J. Hoh,et al.  AFM force measurements on microtubule‐associated proteins: the projection domain exerts a long‐range repulsive force , 2001, FEBS letters.

[416]  A. M. Ruvinsky,et al.  Novel statistical‐thermodynamic methods to predict protein‐ligand binding positions using probability distribution functions , 2005, Proteins.

[417]  W. Lipscomb,et al.  Recent Advances in Zinc Enzymology , 1997 .

[418]  P. Tompa.  Intrinsically unstructured proteins. , 2002, Trends in biochemical sciences.

[419]  L. Hengst,et al.  p27 binds cyclin–CDK complexes through a sequential mechanism involving binding-induced protein folding , 2004, Nature Structural &Molecular Biology.

[420]  M. Lambert,et al.  Activation of nuclear receptors: a perspective from structural genomics. , 2003, Structure.

[421]  Robert B. Russell,et al.  GlobPlot: exploring protein sequences for globularity and disorder , 2003, Nucleic Acids Res..

[422]  D. Eliezer,et al.  Conformational properties of alpha-synuclein in its free and lipid-associated states. , 2001, Journal of molecular biology.

[423]  M. Lemmon,et al.  Membrane recognition by phospholipid-binding domains , 2008, Nature Reviews Molecular Cell Biology.

[424]  Joël Janin.  Structural genomics: winning the second half of the game. , 2007, Structure.

[425]  A. Nassar,et al.  Improving the decision-making process in structural modification of drug candidates: reducing toxicity. , 2004, Drug discovery today.

[426]  Maria Kontoyianni,et al.  Evaluation of library ranking efficacy in virtual screening , 2005, J. Comput. Chem..

[427]  Paul M. Selzer,et al.  The Impact of Tautomer Forms on Pharmacophore-Based Virtual Screening , 2006, J. Chem. Inf. Model..

[428]  B. Dahlbäck,et al.  Involvement of Lys 62[217] and Lys 63[218] of Human Anticoagulant Protein C in Heparin Stimulation of Inhibition by the Protein C Inhibitor , 1999, Thrombosis and Haemostasis.

[429]  Thomas Bäck,et al.  The Molecule Evoluator. An Interactive Evolutionary Algorithm for the Design of Drug-Like Molecules , 2006, J. Chem. Inf. Model..

[430]  Jessica H. Fong,et al.  Modeling the evolution of protein domain architectures using maximum parsimony. , 2007, Journal of molecular biology.

[431]  J. Onuchic,et al.  The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. , 2000, Advances in protein chemistry.

[432]  Ajay N. Jain,et al.  Scoring functions for protein-ligand docking. , 2006, Current protein & peptide science.

[433]  Mikko J. Vainio,et al.  Similarity based virtual screening: a tool for targeted library design. , 2006, Journal of medicinal chemistry.

[434]  V. Uversky.  Alpha-synuclein misfolding and neurodegenerative diseases. , 2008, Current protein & peptide science.

[435]  H. Dyson,et al.  Coupling of folding and binding for unstructured proteins. , 2002, Current opinion in structural biology.

[436]  Vladimir Vacic,et al.  Composition Profiler: a tool for discovery and visualization of amino acid composition differences , 2007, BMC Bioinformatics.

[437]  P. Goodford.  A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. , 1985, Journal of medicinal chemistry.

[438]  P. Privalov.  Stability of proteins: small globular proteins. , 1979, Advances in protein chemistry.

[439]  N. Baurin.  Drug-Like Annotation and Duplicate Analysis of a 23-Supplier Chemical Database Totalling 2.7 Million Compounds. , 2004 .

[440]  Thierry Langer,et al.  Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-Scale Survey on the Retrieval of Protein-Bound Ligand Conformations. , 2006 .

[441]  Y. Martin,et al.  A general and fast scoring function for protein-ligand interactions: a simplified potential approach. , 1999, Journal of medicinal chemistry.

[442]  Albert H. Mao,et al.  Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins. , 2008, Journal of the American Chemical Society.

[443]  E. Koonin,et al.  Evolution of gene fusions: horizontal transfer versus independent events , 2002, Genome Biology.

[444]  Ilya A Vakser.  PSI has to live and become PCI: Protein Complex Initiative. , 2008, Structure.

[445]  Hans-Joachim Böhm,et al.  LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads , 1992, J. Comput. Aided Mol. Des..

[446]  Ferran Sanz,et al.  3D-QSAR methods on the basis of ligand–receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 ligands , 2000, J. Comput. Aided Mol. Des..

[447]  K. Dill,et al.  From Levinthal to pathways to funnels , 1997, Nature Structural Biology.

[448]  Pengyu Y. Ren,et al.  Calculation of protein–ligand binding free energy by using a polarizable potential , 2008, Proceedings of the National Academy of Sciences.

[449]  S. Wodak,et al.  Assessment of CAPRI predictions in rounds 3–5 shows progress in docking procedures , 2005, Proteins.

[450]  O. Lichtarge,et al.  Evolutionary predictions of binding surfaces and interactions. , 2002, Current opinion in structural biology.

[451]  Tal Pupko,et al.  Structural Genomics , 2005 .

[452]  Nico P E Vermeulen.  Prediction of drug metabolism: the case of cytochrome P450 2D6. , 2003, Current topics in medicinal chemistry.

[453]  Itay Mayrose,et al.  Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues , 2002, ISMB.

[454]  Irene T. Weber,et al.  The structure of the E. coli recA protein monomer and polymer , 1992, Nature.

[455]  Luhua Lai,et al.  PSI‐DOCK: Towards highly efficient and accurate flexible ligand docking , 2006, Proteins.

[456]  J. Onuchic,et al.  Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[457]  R. Abagyan,et al.  Type-II kinase inhibitor docking, screening, and profiling using modified structures of active kinase states. , 2008, Journal of medicinal chemistry.

[458]  M Hendlich,et al.  LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. , 1997, Journal of molecular graphics & modelling.

[459]  S. Sharma,et al.  Protein-protein interactions: lessons learned. , 2002, Current medicinal chemistry. Anti-cancer agents.

[460]  Christopher J. Oldfield,et al.  Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. , 2007, Journal of proteome research.

[461]  M. Karplus,et al.  Functionality maps of binding sites: A multiple copy simultaneous search method , 1991, Proteins.

[462]  S. Vajda,et al.  Anchor residues in protein-protein interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[463]  J. V. Moran,et al.  Exon shuffling by L1 retrotransposition. , 1999, Science.

[464]  D. Ringe,et al.  Locating and characterizing binding sites on proteins , 1996, Nature Biotechnology.

[465]  Arthur Dalby,et al.  Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited , 1992, J. Chem. Inf. Comput. Sci..

[466]  L. Moore,et al.  Structural determinants of ligand binding selectivity between the peroxisome proliferator-activated receptors , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[467]  Didier Rognan,et al.  ConsDock: A new program for the consensus analysis of protein–ligand interactions , 2002, Proteins.

[468]  Dannie Durand,et al.  Graph Theoretical Insights into Evolution of Multidomain Proteins , 2005, RECOMB.

[469]  D. Lane,et al.  p53, guardian of the genome , 1992, Nature.

[470]  Maria Kontoyianni,et al.  Evaluation of docking performance: comparative data on docking algorithms. , 2004, Journal of medicinal chemistry.

[471]  R. Abagyan,et al.  Identification of protein-protein interaction sites from docking energy landscapes. , 2004, Journal of molecular biology.

[472]  F. Guerlesquin,et al.  Protein–protein interaction inhibition (2P2I) combining high throughput and virtual screening: Application to the HIV-1 Nef protein , 2007, Proceedings of the National Academy of Sciences.

[473]  Niu Huang,et al.  Physics-Based Scoring of Protein-Ligand Complexes: Enrichment of Known Inhibitors in Large-Scale Virtual Screening , 2006, J. Chem. Inf. Model..

[474]  John Moult,et al.  Comparative modeling in structural genomics. , 2008, Structure.

[475]  P Willett,et al.  Development and validation of a genetic algorithm for flexible docking. , 1997, Journal of molecular biology.

[476]  Tom Halgren,et al.  New Method for Fast and Accurate Binding‐site Identification and Analysis , 2007, Chemical biology & drug design.

[477]  J. Schwabe,et al.  Mechanism of the nuclear receptor molecular switch. , 2004, Trends in biochemical sciences.

[478]  R. Russell,et al.  Linear motifs: Evolutionary interaction switches , 2005, FEBS letters.

[479]  G A Petsko,et al.  Study of protein dynamics by X-ray diffraction. , 1986, Methods in enzymology.

[480]  Francisco Torrens,et al.  A new topological descriptors based model for predicting intestinal epithelial transport of drugs in Caco-2 cell culture. , 2004, Journal of pharmacy & pharmaceutical sciences : a publication of the Canadian Society for Pharmaceutical Sciences, Societe canadienne des sciences pharmaceutiques.

[481]  Nicholas H. Putnam,et al.  The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans , 2008, Nature.

[482]  J. Fleckner,et al.  Synthesis and biological and structural characterization of the dual-acting peroxisome proliferator-activated receptor alpha/gamma agonist ragaglitazar. , 2003, Journal of medicinal chemistry.

[483]  Gideon Schreiber,et al.  Similar chemistry, but different bond preferences in inter versus intra‐protein interactions , 2008, Proteins.

[484]  Cédric Kalinski,et al.  Isoquinolin‐1‐one Inhibitors of the MDM2–p53 Interaction , 2008, ChemMedChem.

[485]  V. Uversky.  Natively unfolded proteins: A point where biology waits for physics , 2002, Protein science : a publication of the Protein Society.

[486]  Wolfgang Guba,et al.  Computational chemistry as an integral component of lead generation. , 2005, Mini reviews in medicinal chemistry.

[487]  P. Tompa,et al.  Fuzzy complexes: polymorphism and structural disorder in protein-protein interactions. , 2008, Trends in biochemical sciences.

[488]  Alice Stanton,et al.  Structure-based design of aliskiren, a novel orally effective renin inhibitor. , 2003, Biochemical and biophysical research communications.

[489]  R. Clark,et al.  Consensus scoring for ligand/protein interactions. , 2002, Journal of molecular graphics & modelling.

[490]  Obradovic,et al.  Predicting Protein Disorder for N-, C-, and Internal Regions. , 1999, Genome informatics. Workshop on Genome Informatics.

[491]  David S. Goodsell,et al.  Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling , 2003, J. Comput. Aided Mol. Des..

[492]  V. Uversky,et al.  Denatured collapsed states in protein folding: Example of apomyoglobin , 2001, Proteins.

[493]  George Karypis,et al.  Indirect Similarity Based Methods for Effective Scaffold-Hopping in Chemical Compounds , 2008, J. Chem. Inf. Model..

[494]  C. Chothia,et al.  The structure of protein-protein recognition sites. , 1990, The Journal of biological chemistry.

[495]  Kevin R. Thornton,et al.  The origin of new genes: glimpses from the young and old , 2003, Nature Reviews Genetics.

[496]  T. Willson,et al.  Asymmetry in the PPARgamma/RXRalpha crystal structure reveals the molecular basis of heterodimerization among nuclear receptors. , 2000, Molecular cell.

[497]  Ronald Wetzel,et al.  Fluorescence correlation spectroscopy shows that monomeric polyglutamine molecules form collapsed structures in aqueous solutions , 2006, Proceedings of the National Academy of Sciences.

[498]  D. Goodsell,et al.  Automated docking of substrates to proteins by simulated annealing , 1990, Proteins.

[499]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[500]  M. Lemmon,et al.  Pleckstrin homology (PH) domains and phosphoinositides. , 2007, Biochemical Society symposium.

[501]  B. Katzenellenbogen,et al.  Allosteric control of ligand selectivity between estrogen receptors alpha and beta: implications for other nuclear receptors. , 2004, Molecular cell.

[502]  A. Nassar,et al.  Strategies for dealing with metabolite elucidation in drug discovery and development. , 2004, Drug discovery today.

[503]  E. Kandel,et al.  A Neuronal Isoform of the Aplysia CPEB Has Prion-Like Properties , 2003, Cell.

[504]  S. Teichmann,et al.  The evolution of domain arrangements in proteins and interaction networks , 2005, Cellular and Molecular Life Sciences CMLS.

[505]  Ruben Abagyan,et al.  Computational identification of novel peripheral protein-membrane interactions , 2008 .

[506]  Haruki Nakamura,et al.  Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks , 2006, FEBS letters.

[507]  F. Lombardo,et al.  Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. , 2001, Advanced drug delivery reviews.

[508]  D. Lancet,et al.  Modular genes with metazoan-specific domains have increased tissue specificity. , 2005, Trends in genetics : TIG.

[509]  Kaushal Rege,et al.  High-throughput screening and quantitative structure-efficacy relationship models of potential displacer molecules for ion-exchange systems. , 2002, Biotechnology and bioengineering.

[510]  V. Helms,et al.  Transient pockets on protein surfaces involved in protein-protein interaction. , 2007, Journal of medicinal chemistry.

[511]  Richard J. Edwards,et al.  SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent , 2006, Nucleic acids research.

[512]  A Keith Dunker,et al.  Intrinsic disorder in scaffold proteins: getting more from less. , 2008, Progress in biophysics and molecular biology.

[513]  Sandor Vajda,et al.  Protein-protein association kinetics and protein docking. , 2002, Current Opinion in Structural Biology.

[514]  Peter Tompa,et al.  Structural disorder promotes assembly of protein complexes , 2007, BMC Structural Biology.

[515]  D. Hartl,et al.  Selective sweep of a newly evolved sperm-specific gene in Drosophila , 1998, Nature.

[516]  Sonia Longhi,et al.  The C-terminal Domain of the Measles Virus Nucleoprotein Is Intrinsically Disordered and Folds upon Binding to the C-terminal Moiety of the Phosphoprotein* , 2003, The Journal of Biological Chemistry.

[517]  O. Ptitsyn,et al.  "Partly folded" state, a new equilibrium state of protein molecules: four-state guanidinium chloride-induced unfolding of beta-lactamase at low temperature. , 1994, Biochemistry.

[518]  J. A. Grant,et al.  A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction. , 2005, Journal of medicinal chemistry.

[519]  A. Grigoriev,et al.  Protein domains correlate strongly with exons in multiple eukaryotic genomes--evidence of exon shuffling? , 2004, Trends in genetics : TIG.

[520]  Luc Morin-Allory,et al.  Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors. , 2005, Journal of medicinal chemistry.

[521]  J. Thornton,et al.  Diversity of protein–protein interactions , 2003, The EMBO journal.

[522]  J. Mason,et al.  Library design using BCUT chemistry-space descriptors and multiple four-point pharmacophore fingerprints: simultaneous optimization and structure-based diversity. , 2000, Journal of molecular graphics & modelling.

[523]  Peter E Wright,et al.  Elucidation of the protein folding landscape by NMR. , 2005, Methods in enzymology.

[524]  X. Barril,et al.  Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. , 2005, Journal of medicinal chemistry.

[525]  P. Toogood.  Inhibition of protein-protein association by small molecules: approaches and progress. , 2002, Journal of medicinal chemistry.

[526]  Pinak Chakrabarti,et al.  Hydration of protein–protein interfaces , 2005, Proteins.

[527]  Jie Liang,et al.  CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues , 2006, Nucleic Acids Res..

[528]  Richard M. Jackson,et al.  Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites , 2005, Bioinform..

[529]  Donald J Abraham,et al.  A nonpeptidic sulfonamide inhibits the p53-mdm2 interaction and activates p53-dependent transcription in mdm2-overexpressing cells. , 2004, Journal of medicinal chemistry.

[530]  Peter Tompa,et al.  The role of structural disorder in the function of RNA and protein chaperones , 2004, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[531]  R. Abagyan,et al.  Predictions of protein flexibility: First‐order measures , 2004, Proteins.

[532]  Christopher J. Oldfield,et al.  Intrinsic disorder and functional proteomics. , 2007, Biophysical journal.

[533]  R. Abagyan,et al.  Comprehensive identification of "druggable" protein ligand binding sites. , 2004, Genome informatics. International Conference on Genome Informatics.

[534]  Ruben Abagyan,et al.  Detailed ab initio prediction of lysozyme–antibody complex with 1.6 Å accuracy , 1994, Nature Structural Biology.

[535]  P. Labute.  A widely applicable set of descriptors. , 2000, Journal of molecular graphics & modelling.

[536]  R. Friesner,et al.  Novel procedure for modeling ligand/receptor induced fit effects. , 2006, Journal of medicinal chemistry.