Bibliography
- Guido RV, Oliva G, Andricopulo AD. Virtual screening and its integration with modern drug design technologies. Curr Med Chem 2008;15(1):37-46
- Lyne PD. Structure-based virtual screening: an overview. Drug Discov Today 2002;7(20):1047-55
- Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nat Rev 2005;4(8):649-63
- Senderowitz H, Marantz Y. G protein-coupled receptors: target-based in silico screening. Curr Pharm Des 2009;15(35):4049-68
- Shoichet BK. Virtual screening of chemical libraries. Nature 2004;432(7019):862-5
- Stahl M, Rarey M. Detailed analysis of scoring functions for virtual screening. J Med Chem 2001;44(7):1035-42
- Villoutreix BO, Eudes R, Miteva MA. Structure-based virtual ligand screening: recent success stories. Comb Chem High Throughput Screen 2009;12(10):1000-16
- Krovat EM, Steindl T, Langer T. Recent advances in docking and scoring. Curr Comput Aided Drug Des 2005;1:93-102
- Bohacek RS, McMartin C, Guida WC. The art and practice of structure-based drug design: a molecular modeling perspective. Medicinal research reviews 1996;16(1):3-50
- Berman HM, Westbrook J, Feng Z, The protein data bank. Nucleic acids research 2000;28(1):235-42
- Kroemer RT. Structure-based drug design: docking and scoring. Curr Protein Pept Sci 2007;8(4):312-28
- Edgar SJ, Holliday JD, Willett P. Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures. J Mol Graph Model 2000;18(4-5):343-57
- Pozzan A. Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery. Curr Pharm Des 2006;12(17):2099-110
- Dixon SL, Smondyrev AM, Knoll EH, PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 2006;20(10-11):647-71
- Guner OF. The impact of pharmacophore modeling in drug design. IDrugs 2005;8(7):567-72
- Wolber G, Seidel T, Bendix F, Langer T. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug discovery today 2008;13(1-2):23-9
- Cramer RD III, Patterson DE, Bunce JD. Recent advances in comparative molecular field analysis (CoMFA). Prog Clin Biol Res 1989;291:161-5
- Tropsha A, Golbraikh A. Predictive QSAR modeling workflow, model applicability domains, and virtual screening. Curr Pharm Des 2007;13(34):3494-504
- Evers A, Hessler G, Matter H, Klabunde T. Virtual screening of biogenic amine-binding G-protein coupled receptors: comparative evaluation of protein- and ligand-based virtual screening protocols. J Med Chem 2005;48(17):5448-65
- Hawkins PC, Skillman AG, Nicholls A. Comparison of shape-matching and docking as virtual screening tools. J Med Chem 2007;50(1):74-82
- McGaughey GB, Sheridan RP, Bayly CI, Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model 2007;47(4):1504-19
- Perez-Nueno VI, Ritchie DW, Rabal O, Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking. J Chem Inf Model 2008;48(3):509-33
- Tan L, Geppert H, Sisay MT, Integrating structure- and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets. ChemMedChem 2008;3(10):1566-71
- Kruger DM, Evers A. Comparison of structure- and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. ChemMedChem 2009;5(1):148-58
- Diller DJ, Merz KM Jr. Can we separate active from inactive conformations? J Comput Aided Mol Des 2002;16(2):105-12
- Koshland DE. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958;44(2):98-104
- Perola E, Charifson PS. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem 2004;47(10):2499-510
- Musafia B, Senderowitz H. Bioactive conformational biasing: a new method for focusing conformational ensembles on bioactive-like conformers. J Chem Inf Model 2009;49(11):2469-80
- Hasegawa K, Arakawa M, Funatsu K. Simultaneous determination of bioactive conformations and alignment rules by multi-way PLS modeling. Comput Biol Chem 2003;27(3):211-16
- Leite TB, Gomes D, Miteva MA, Frog: a FRee Online druG 3D conformation generator. Nucleic Acids Res 2007;35(Web Server issue):W568-72
- Liu X, Bai F, Ouyang S, Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. BMC Bioinformatics 2009;10:101
- Tresadern G, Agrafiotis DK. Conformational sampling with stochastic proximity embedding and self-organizing superimposition: establishing reasonable parameters for their practical use. J Chem Inf Model 2009;49(12):2786-800
- Sperandio O, Souaille M, Delfaud F, MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. Eur J Med Chem 2009;44(4):1405-9
- Foloppe N, Chen IJ. Conformational sampling and energetics of drug-like molecules. Curr Med Chem 2009;16(26):3381-413
- Bostrom J, Grant A. Exploring ligand conformations in drug design. In: Mannhold R, Kubinyi H, Folkers G, editors. Molecular drug properties, measurement and prediction. Wiley-VCH, Weinheim: 2007:183-206
- Gund P. Pharmacophoric pattern searching and receptor matching. Annu Rep Med Chem 1979;14:299-308
- Pearlman RS. Rapid generation of high quality approximate 3D molecular structures. Chem Des Automot News 1987;2(1):5-7
- Gasteiger J, Rudolph C, Sadowski J. Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comp Methodol 1990;3:537-47
- Kearsley SK, Smith GM. An alternative method for the alignment of molecular structures: maximizing electrostatic and steric overlap. Tetrahedron Comp Methodol 1990;3(6):615-33
- Kuntz ID, Blaney JM, Oatley SJ, A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161(2):269-88
- Van Drie JH, Weininger D, Martin YC. ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures. J Comput Aided Mol Des 1989;3(3):225-51
- Kearsley SK, Underwood DJ, Sheridan RP, Miller MD. Flexibases: a way to enhance the use of molecular docking methods. J Comput Aided Mol Des 1994;8(5):565-82
- Miller MD, Kearsley SK, Underwood DJ, Sheridan RP. FLOG: a system to select ‘quasi-flexible’ ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 1994;8(2):153-74
- Leach AR, Dolata DP, Prout K. Automated conformational analysis and structure generation: algorithms for molecular perception. J Chem Inf Comput Sci 1990;30(3):316-24
- Mohamadi F, Richards NGJ, Guida WC, Macromodel – an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J Comput Chem 1990;11(4):440-67
- Kolossvary I, Guida WC. Low mode search. An efficient, automated computational method for conformational analysis: application to cyclic and acyclic alkanes and cyclic peptides. J Am Chem Soc 1996;118(21):5011-19
- ROTATE is available from Molecular Networks Erlagen, Germany. Available from: http://www. molecular-networks.com
- OMEGA is available from OpenEye Scientific Software Inc. Santa Fe, NM, USA. Available from: http://www.eyesopen.com
- Catalyst is available from Accelrys, Inc. San Diego, CA, USA. Available from: http://www.accelrys.com
- FRED is available from OpenEye Scientific Software, Inc. Santa Fe, NM, USA. Available from: http://www.eyesopen.com
- Sauton N, Lagorce D, Villoutreix BO, Miteva MA. MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics 2008;9:184
- ROCS is available from OpenEye Scientific Software Inc. Santa Fe, NM, USA. Available from: http://www.eyesopen.com
- Schlosser J, Rarey M. Beyond the virtual screening paradigm: structure-based searching for new lead compounds. J Chem Inf Model 2009;49(4):800-9
- Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009;5(11):789-96
- Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: “what you see” is not always “what you get”. Structure 2009;17(4):489-98
- Gunther S, Senger C, Michalsky E, Representation of target-bound drugs by computed conformers: implications for conformational libraries. BMC Bioinformatics 2006;7:293
- Takagi T, Amano M, Tomimoto M. Novel method for the evaluation of 3D conformation generators. J Chem Inf Model 2009;49(6):1377-88
- Griewel A, Kayser O, Schlosser J, Rarey M. Conformational sampling for large-scale virtual screening: accuracy versus ensemble size. J Chem Inf Model 2009;49(10):2303-11
- Nicklaus MC, Wang S, Driscoll JS, Milne GW. Conformational changes of small molecules binding to proteins. Bioorg Med Chem 1995;3(4):411-28
- Guvench O, Price DJ, Brooks CL, III. Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins 2005;58(2):407-17
- Bostrom J, Norrby PO, Liljefors T. Conformational energy penalties of protein-bound ligands. J Comput Aided Mol Des 1998;12(4):383-96
- Butler KT, Luque FJ, Barril X. Toward accurate relative energy predictions of the bioactive conformation of drugs. J Comput Chem 2009;30(4):601-10
- MOE is available from Chemical Computing Group, Montreal, Quebec, Canada. Available from: http://www.chemcomp.com
- Bostrom J. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. J Comput Aided Mol Des 2001;15(12):1137-52
- McMartin C, Bohacek RS. Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: comparison of predicted and experimental conformations of inhibitors of three enzymes. J Comput Aided Mol Des 1995;9(3):237-50
- McMartin C, Bohacek RS. QXP: powerful, rapid computer algorithms for structure-based drug design. J Comput Aided Mol Des 1997;11(4):333-44
- Bostrom J, Greenwood JR, Gottfries J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model 2003;21(5):449-62
- Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235(3):983-1002
- Chen IJ, Foloppe N. Conformational sampling of drug like molecules with MOE and catalyst: implications for pharmacophore modeling and virtual screening. J Chem Inf Model 2008;48(9):1773-91
- Dorfman RJ, Smith KM, Masek BB, Clark RD. A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers. J Comput Aided Mol Des 2008;22(9):681-91
- Chen IJ, Foloppe N. Drug-like bioactive structures and conformational coverage with the LigPrep/ConfGen suite: comparison to programs MOE and catalyst. J Chem Inf Model 2010;50(5):822-39
- Kirchmair J, Laggner C, Wolber G, Langer T. Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms. J Chem Inf Model 2005;45(2):422-30
- Li J, Ehlers T, Sutter J, CAESAR: a new conformer generation algorithm based on recursive build up and local rotational symmetry consideration. J Chem Inf Model 2007;47(5):1923-32
- Vainio MJ, Johnson MS. Generating conformer ensembles using a multiobjective genetic algorithm. J Chem Inf Model 2007;47(6):2462-74
- Borodina YV, Bolton E, Fontaine F, Bryant SH. Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. J Chem Inf Model 2007;47(4):1428-37
- Smellie A, Kahn SD, Teig SL. Analysis of conformational coverage. 1. Validation and estimation of coverage. J Chem Inf Comput Sci 1995;35(2):285-94
- Smellie A, Kahn SD, Teig SL. Analysis of conformational coverage. 2. applications of conformational models. J Chem Inf Comput Sci 1995;35(2):295-304
- Koshland DE Jr. Correlation of structure and function in enzyme action. Science 1963;142:1533-41
- Koshland DE Jr. Conformation changes at the active site during enzyme Action. Fed Proc 1964;23:719-26
- Yankeelov JA Jr, Koshland DE Jr. Evidence for conformation changes induced by substrates of phosphoglucomutase. J Biol Chem 1965;240:1593-602
- Wang Q, Pang YP. Preference of small molecules for local minimum conformations when binding to proteins. PLoS One 2007;2(9):e820
- Vieth M, Hirst JD, Brooks CL III. Do active site conformations of small ligands correspond to low free-energy solution structures? J Comput Aided Mol Des 1998;12(6):563-72
- Tirado-Rives J, Jorgensen WL. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J Med Chem 2006;49(20):5880-4
- Yongye AB, Bender A, Martinez-Mayorga K. Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. J Comput Aided Mol Des 2010;24(8):675-86
- Stockwell GR, Thornton JM. Conformational diversity of ligands bound to proteins. J Mol Biol 2006;356(4):928-44
- Klucik J, Xiao YD, Hammond PS, Targacept active conformation search: a new method for predicting the conformation of a ligand bound to its protein target. J Med Chem 2004;47(27):6831-9
- Auer J, Bajorath J. Distinguishing between bioactive and modeled compound conformations through mining of emerging chemical patterns. J Chem Inf Model 2008;48(9):1747-53
- Michalsky E, Dunkel M, Goede A, Preissner R. SuperLigands – a database of ligand structures derived from the protein data bank. BMC Bioinformatics 2005;6:122
- Izrailev S, Zhu F, Agrafiotis DK. A distance geometry heuristic for expanding the range of geometries sampled during conformational search. J Comput Chem 2006;27(16):1962-9
- Xu H, Izrailev S, Agrafiotis DK. Conformational sampling by self-organization. J Chem Inf Comput Sci 2003;43(4):1186-91
- Agrafiotis DK, Gibbs AC, Zhu F, Conformational sampling of bioactive molecules: a comparative study. J Chem Inf Model 2007;47(3):1067-86
- Rubicon is available from daylight chemical information systems, Inc. Aliso Viejo, CA, USA. Available from: http://www.daylight.com
- Sadowski J, Bostrom J. MIMUMBA revisited: torsion angle rules for conformer generation derived from X-ray structures. J Chem Inf Model 2006;46(6):2305-9
- Allen FH. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B 2002;58(Pt 3 Pt 1):380-8
- Hao MH, Haq O, Muegge I. Torsion angle preference and energetics of small-molecule ligands bound to proteins. J Chem Inf Model 2007;47(6):2242-52
- Brameld KA, Kuhn B, Reuter DC, Stahl M. Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis. J Chem Inf Model 2008;48(1):1-24
- Diago LA, Morell P, Aguilera L, Moreno E. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. BMC Bioinformatics 2007;8:310
- Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006;49(23):6789-801
- Watts KS, Dalal P, Murphy RB, ConfGen: a conformational search method for efficient generation of bioactive conformers. J Chem Inf Model 2010;50(4):534-46
- Pearlman RS, Balducci R. Confort: a novel algorithm for conformational analysis. National Meeting of the American Chemical Society 1998