Keynote review: Structural biology and drug discovery
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[1] Eric F. Johnson,et al. The Structure of Human Microsomal Cytochrome P450 3A4 Determined by X-ray Crystallography to 2.05-Å Resolution* , 2004, Journal of Biological Chemistry.
[2] Stanislav Miertus,et al. Combinatorial chemistry and high-throughput screening in drug discovery: Different strategies and formats , 2004, Molecular Diversity.
[3] T. Blundell,et al. Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.
[4] J Moult,et al. Analysis of the steric strain in the polypeptide backbone of protein molecules , 1991, Proteins.
[5] R Miller,et al. Optimizing Shake-and-Bake for proteins. , 1999, Acta crystallographica. Section D, Biological crystallography.
[6] Paul D Lyne,et al. Structure-based virtual screening: an overview. , 2002, Drug discovery today.
[7] B. Shoichet,et al. Soft docking and multiple receptor conformations in virtual screening. , 2004, Journal of medicinal chemistry.
[8] T. O'Brien,et al. Fragment-based drug discovery. , 2004, Journal of medicinal chemistry.
[9] William R. Taylor,et al. A structural model for the retroviral proteases , 1987, Nature.
[10] M. Swindells,et al. Protein clefts in molecular recognition and function. , 1996, Protein science : a publication of the Protein Society.
[11] Bernhard Rupp. High-throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility. , 2003, Accounts of chemical research.
[12] Tom L. Blundell,et al. Insulin: The Structure in the Crystal and its Reflection in Chemistry and Biology by , 1972 .
[13] T. Blundell. Structure-based drug design. , 1996, Nature.
[14] D. Diller,et al. Kinases, homology models, and high throughput docking. , 2003, Journal of medicinal chemistry.
[15] 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.
[16] Christopher W Murray,et al. Fragment-based lead discovery using X-ray crystallography. , 2005, Journal of medicinal chemistry.
[17] Lance Stewart,et al. High-throughput crystallization and structure determination in drug discovery. , 2002, Drug discovery today.
[18] Peter Traxler,et al. Phenylamino-pyrimidine (PAP) — derivatives: a new class of potent and highly selective PDGF-receptor autophosphorylation inhibitors , 1996 .
[19] Krystal J Alligood,et al. A Unique Structure for Epidermal Growth Factor Receptor Bound to GW572016 (Lapatinib) , 2004, Cancer Research.
[20] D. Fabbro,et al. Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. , 2003, Journal of medicinal chemistry.
[21] John P. Overington,et al. X-ray analysis of HIV-1 proteinase at 2.7 Å resolution confirms structural homology among retroviral enzymes , 1989, Nature.
[22] T. Blundell,et al. Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. , 1987, Protein engineering.
[23] D W Cushman,et al. Design of potent competitive inhibitors of angiotensin-converting enzyme. Carboxyalkanoyl and mercaptoalkanoyl amino acids. , 1977, Biochemistry.
[24] H. Jhoti,et al. Structure-based screening of low-affinity compounds. , 2002, Drug discovery today.
[25] A. W. Dean,et al. Solution‐Phase Combinatorial Chemistry in Lead Discovery , 1998 .
[26] John P. Overington,et al. Alignment and searching for common protein folds using a data bank of structural templates. , 1993, Journal of molecular biology.
[27] James F Blake,et al. Structure-based generation of viable leads from small combinatorial libraries. , 2004, Current opinion in drug discovery & development.
[28] Thomas Lengauer,et al. Flexible docking under pharmacophore type constraints , 2002, J. Comput. Aided Mol. Des..
[29] M. Congreve,et al. Fragment-based lead discovery , 2004, Nature Reviews Drug Discovery.
[30] J. Whisstock,et al. Protein structural alignments and functional genomics , 2001, Proteins.
[31] B. Shoichet,et al. Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. , 2002, Journal of medicinal chemistry.
[32] D. Kostrewa,et al. Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. , 2000, Journal of medicinal chemistry.
[33] R. Spencer,et al. High-throughput screening of historic collections: observations on file size, biological targets, and file diversity. , 1998, Biotechnology and bioengineering.
[34] George M Sheldrick,et al. [37] Patterson superposition and ab initio phasing. , 1997, Methods in enzymology.
[35] Tom L Blundell,et al. High-throughput X-ray crystallography for drug discovery. , 2004, Current opinion in pharmacology.
[36] O. Witte,et al. The BCR-ABL story: bench to bedside and back. , 2004, Annual review of immunology.
[37] L. Pustilnik,et al. Inhibition of epidermal growth factor receptor-associated tyrosine phosphorylation in human carcinomas with CP-358,774: dynamics of receptor inhibition in situ and antitumor effects in athymic mice. , 1999, The Journal of pharmacology and experimental therapeutics.
[38] K. Parang,et al. Design strategies for protein kinase inhibitors. , 2004, Current opinion in drug discovery & development.
[39] J. Irwin,et al. Lead discovery using molecular docking. , 2002, Current opinion in chemical biology.
[40] Aled Edwards,et al. High-throughput protein crystallization. , 2003, Journal of structural biology.
[41] A. Hopkins,et al. Ligand efficiency: a useful metric for lead selection. , 2004, Drug discovery today.
[42] Philip M. Dean,et al. A validation study on the practical use of automated de novo design , 2002, J. Comput. Aided Mol. Des..
[43] L. Wodicka,et al. A small molecule–kinase interaction map for clinical kinase inhibitors , 2005, Nature Biotechnology.
[44] P J Goodford,et al. COMPOUNDS DESIGNED TO FIT A SITE OF KNOWN STRUCTURE IN HUMAN HAEMOGLOBIN , 1976, British journal of pharmacology.
[45] Ajay,et al. The SHAPES strategy: an NMR-based approach for lead generation in drug discovery. , 1999, Chemistry & biology.
[46] K. Büssow,et al. An automated method for high-throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography , 2003, BMC biotechnology.
[47] Philip M Dean,et al. De novo drug design: integration of structure-based and ligand-based methods. , 2004, Current opinion in drug discovery & development.
[48] P. Goodford,et al. THE INTERACTION OF HUMAN HAEMOGLOBIN WITH ALLOSTERIC EFFECTORS AS A MODEL FOR DRUG‐RECEPTOR INTERACTIONS , 1980, British journal of pharmacology.
[49] Christopher W Murray,et al. Identification of novel p38alpha MAP kinase inhibitors using fragment-based lead generation. , 2005, Journal of medicinal chemistry.
[50] D. M. Ryan,et al. Rational design of potent sialidase-based inhibitors of influenza virus replication , 1993, Nature.
[51] A. Hopkins,et al. The druggable genome , 2002, Nature Reviews Drug Discovery.
[52] K Fujikawa,et al. The coagulation cascade: initiation, maintenance, and regulation. , 1991, Biochemistry.
[53] Robin Taylor,et al. A new test set for validating predictions of protein–ligand interaction , 2002, Proteins.
[54] O. Lichtarge,et al. Evolutionary predictions of binding surfaces and interactions. , 2002, Current opinion in structural biology.
[55] P. Argos,et al. Strain in protein structures as viewed through nonrotameric side chains: II. effects upon ligand binding , 1999, Proteins.
[56] B. L. Sibanda,et al. Three-dimensional structure, specificity and catalytic mechanism of renin , 1983, Nature.
[57] John P. Overington,et al. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction , 1990, Proceedings of the Royal Society of London. Series B: Biological Sciences.
[58] M. Sternberg,et al. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. , 1987, Journal of molecular biology.
[59] Konrad Büssow,et al. Facilities and methods for the high-throughput crystal structural analysis of human proteins. , 2003, Accounts of chemical research.
[60] Jürgen Bajorath,et al. Integration of virtual and high-throughput screening , 2002, Nature Reviews Drug Discovery.
[61] P. Hajduk,et al. Discovering High-Affinity Ligands for Proteins: SAR by NMR , 1996, Science.
[62] Teruki Honma,et al. Recent advances in de novo design strategy for practical lead identification , 2003, Medicinal research reviews.
[63] J J Baldwin,et al. Thienothiopyran-2-sulfonamides: novel topically active carbonic anhydrase inhibitors for the treatment of glaucoma. , 1989, Journal of medicinal chemistry.
[64] E. Lindahl,et al. Identification of related proteins on family, superfamily and fold level. , 2000, Journal of molecular biology.
[65] M C Peitsch,et al. Protein modelling for all. , 1999, Trends in biochemical sciences.
[66] Dale J. Kempf,et al. ABT-378, a Highly Potent Inhibitor of the Human Immunodeficiency Virus Protease , 1998, Antimicrobial Agents and Chemotherapy.
[67] G. Klebe,et al. DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. , 2002, Journal of medicinal chemistry.
[68] M. DePristo,et al. Heterogeneity and inaccuracy in protein structures solved by X-ray crystallography. , 2004, Structure.
[69] Michal Vieth,et al. SDOCKER: a method utilizing existing X-ray structures to improve docking accuracy. , 2004, Journal of medicinal chemistry.
[70] J M Thornton,et al. Three-dimensional structure analysis of PROSITE patterns. , 1999, Journal of molecular biology.
[71] W G Laver,et al. Structure-activity relationship studies of novel carbocyclic influenza neuraminidase inhibitors. , 1998, Journal of medicinal chemistry.
[72] D. T. Jones,et al. A new approach to protein fold recognition , 1992, Nature.
[73] D E McRee,et al. Mammalian microsomal cytochrome P450 monooxygenase: structural adaptations for membrane binding and functional diversity. , 2000, Molecular cell.
[74] M Stahl,et al. Structure-based library design: molecular modelling merges with combinatorial chemistry. , 2000, Current opinion in chemical biology.
[75] Jonathan W. Essex,et al. A review of protein-small molecule docking methods , 2002, J. Comput. Aided Mol. Des..
[76] D Eisenberg,et al. A 3D-1D substitution matrix for protein fold recognition that includes predicted secondary structure of the sequence. , 1997, Journal of molecular biology.
[77] T. Blundell,et al. Distinguishing structural and functional restraints in evolution in order to identify interaction sites. , 2004, Journal of molecular biology.
[78] John A. Lowe,et al. A guide to drug discovery: The role of the medicinal chemist in drug discovery — then and now , 2004, Nature Reviews Drug Discovery.
[79] Amos Bairoch,et al. The PROSITE database, its status in 1999 , 1999, Nucleic Acids Res..
[80] J. Bajorath,et al. Docking and scoring in virtual screening for drug discovery: methods and applications , 2004, Nature Reviews Drug Discovery.
[81] Thomas Lengauer,et al. FlexE: efficient molecular docking considering protein structure variations. , 2001, Journal of molecular biology.
[82] Andrew J. Sharff. HIGH THROUGHPUT CRYSTALLOGRAPHY ON AN IN-HOUSE SOURCE, USING ACTOR , 2003 .
[83] Clive McCarthy,et al. Mapping the kinase domain of Janus Kinase 3. , 2003, Bioorganic & medicinal chemistry letters.
[84] Steven W Muchmore,et al. Crystallography, NMR and virtual screening: integrated tools for drug discovery. , 2003, Current opinion in drug discovery & development.
[85] Darren R. Flower,et al. Drug design : cutting edge approaches , 2002 .
[86] Bohdan Waszkowycz,et al. PRO_SELECT: combining structure-based drug design and array-based chemistry for rapid lead discovery. 2. The development of a series of highly potent and selective factor Xa inhibitors. , 2002, Journal of medicinal chemistry.
[87] Ajay N. Jain,et al. Virtual screening in lead discovery and optimization. , 2004, Current opinion in drug discovery & development.
[88] Jan Pieter Abrahams,et al. The prospects of protein nanocrystallography. , 2002, Acta crystallographica. Section D, Biological crystallography.
[89] A. Jeltsch,et al. High-throughput purification of polyHis-tagged recombinant fusion proteins. , 2003, Methods in molecular biology.
[90] A Wlodawer,et al. Structure of complex of synthetic HIV-1 protease with a substrate-based inhibitor at 2.3 A resolution. , 1989, Science.
[91] Anastassis Perrakis,et al. Automated protein model building combined with iterative structure refinement , 1999, Nature Structural Biology.
[92] N. Chayen,et al. Protein crystallization for genomics: towards high-throughput optimization techniques. , 2002, Acta crystallographica. Section D, Biological crystallography.
[93] R. Dolle. Comprehensive survey of combinatorial library synthesis: 2000. , 2001, Journal of combinatorial chemistry.
[94] A Abrahamsson,et al. The direct thrombin inhibitor melagatran and its oral prodrug H 376/95: intestinal absorption properties, biochemical and pharmacodynamic effects. , 2001, Thrombosis research.
[95] John P. Overington,et al. Knowledge‐based protein modelling and design , 1988 .
[96] Ceslovas Venclovas,et al. Assessment of progress over the CASP experiments , 2003, Proteins.
[97] N C Cohen,et al. Generation of new-lead structures in computer-aided drug design. , 1995, Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques.
[98] Adam Godzik,et al. Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[99] Jürg Zimmermann,et al. Potent and Selective Inhibitors of the AbL-Kinase: Phenylaminopyrimidine (PAP) Derivatives. , 1997 .
[100] I. Kuntz,et al. Molecular docking to ensembles of protein structures. , 1997, Journal of molecular biology.
[101] Martin Stahl,et al. Novel dihydrofolate reductase inhibitors. Structure-based versus diversity-based library design and high-throughput synthesis and screening. , 2003, Journal of medicinal chemistry.
[102] R. Abagyan,et al. Predictions of protein flexibility: First‐order measures , 2004, Proteins.
[103] T. Sawasaki,et al. High-throughput, genome-scale protein production method based on the wheat germ cell-free expression system. , 2003, Biotechnology advances.
[104] R Abagyan,et al. High-throughput docking for lead generation. , 2001, Current opinion in chemical biology.
[105] Anastassis Perrakis,et al. Current state of automated crystallographic data analysis , 2000, Nature Structural Biology.
[106] S. P. Chambers. High-throughput protein expression for the post-genomic era. , 2002, Drug discovery today.
[107] Vicki L. Nienaber,et al. Discovering novel ligands for macromolecules using X-ray crystallographic screening , 2000, Nature Biotechnology.
[108] J F Davies,et al. Viracept (nelfinavir mesylate, AG1343): a potent, orally bioavailable inhibitor of HIV-1 protease. , 1997, Journal of medicinal chemistry.
[109] David C. Jones,et al. GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. , 1999, Journal of molecular biology.
[110] M. Murcko,et al. Crystal Structure of HIV-1 Protease in Complex with Vx-478, a Potent and Orally Bioavailable Inhibitor of the Enzyme , 1995 .
[111] J. Greer,et al. Automated crystal mounting and data collection for protein crystallography. , 2000, Structure.
[112] Jose Cosme,et al. Crystal Structures of Human Cytochrome P450 3A4 Bound to Metyrapone and Progesterone , 2004, Science.
[113] A. Gill,et al. New lead generation strategies for protein kinase inhibitors - fragment based screening approaches. , 2004, Mini reviews in medicinal chemistry.
[114] S F Campbell,et al. Science, art and drug discovery: a personal perspective. , 2000, Clinical science.
[115] Jean-Pierre Marquette,et al. SAR and X-ray. A new approach combining fragment-based screening and rational drug design: application to the discovery of nanomolar inhibitors of Src SH2. , 2002, Journal of medicinal chemistry.
[116] T Lengauer,et al. The particle concept: placing discrete water molecules during protein‐ligand docking predictions , 1999, Proteins.
[117] J. Varghese,et al. Development of neuraminidase inhibitors as anti‐influenza virus drugs , 1999 .
[118] Roland E Dolle,et al. Comprehensive survey of combinatorial library synthesis: 2003. , 2004, Journal of combinatorial chemistry.
[119] D. Fabbro,et al. Structural insights into the conformational selectivity of STI-571 and related kinase inhibitors. , 2004, Current opinion in drug discovery & development.
[120] Zhan Deng,et al. Interaction profiles of protein kinase-inhibitor complexes and their application to virtual screening. , 2005, Journal of medicinal chemistry.
[121] Jeffrey W. Peng,et al. Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design. , 2004, Journal of synchrotron radiation.
[122] 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.
[123] Todd J. A. Ewing,et al. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases , 2001, J. Comput. Aided Mol. Des..
[124] A M Lesk,et al. Domain closure in mitochondrial aspartate aminotransferase. , 1992, Journal of molecular biology.
[125] Jürg Zimmermann,et al. Potent and selective inhibitors of the Abl-kinase: phenylamino-pyrimidine (PAP) derivatives , 1997 .