Cited by 6,763Computational Drug Discovery MethodsProtein Structure and DynamicsProtein Interaction Studies and Fluorescence Analysis

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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

Jones, Gareth, Willett, Peter, Glen, Robert C, Leach, Andrew R, Taylor, Robin·1997·Journal of Molecular Biology

DOI 10.1006/jmbi.1996.0897

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Abstract

Prediction of small molecule binding modes to macromolecules of known three-dimensional structure is a problem of paramount importance in rational drug design (the "docking" problem). We report the development and validation of the program GOLD (Genetic Optimisation for Ligand Docking). GOLD is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand conformational flexibility with partial flexibility of the protein, and satisfies the fundamental requirement that the ligand must displace loosely bound water on binding. Numerous enhancements and modifications have been applied to the original technique resulting in a substantial increase in the reliability and the applicability of the algorithm. The advanced algorithm has been tested on a dataset of 100 complexes extracted from the Brookhaven Protein DataBank. When used to dock the ligand back into the binding site, GOLD achieved a 71% success rate in identifying the experimental binding mode.

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Genetic algorithms in search, optimization, and machine learning
(1989) · Choice Reviews Online · doi:10.5860/choice.27-0936 · Cited by 49,178
Adaptation in Natural and Artificial Systems
Holland, J. H. (1992) · The MIT Press eBooks · doi:10.7551/mitpress/1090.001.0001 · Cited by 47,340
Molecular Theory of Gases and Liquids
Hirschfelder, J. O., Curtiss, C. F., & Bird, R. B. (1955) · Physics Today · doi:10.1063/1.3061949 · Cited by 11,445
The protein data bank: A computer-based archival file for macromolecular structures
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., & Tasumi, M. (1977) · Journal of Molecular Biology · doi:10.1016/s0022-2836(77)80200-3 · Cited by 8,574
Molecular theory of gases and liquids
Scott, R. L. (1955) · Journal of Chemical Education · doi:10.1021/ed032p232.2 · Cited by 3,958
Semianalytical treatment of solvation for molecular mechanics and dynamics
Still, W. C., Tempczyk, A., Hawley, R. C., & Hendrickson, T. F. (1990) · Journal of the American Chemical Society · doi:10.1021/ja00172a038 · Cited by 3,653
A Fast Flexible Docking Method using an Incremental Construction Algorithm
Rarey, M., Kramer, B., Lengauer, T., & Klebe, G. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0477 · Cited by 2,836
Validation of the general purpose tripos 5.2 force field
Clark, M., CRAMER, R. D. I., & Opdenbosch, N. V. (1989) · Journal of Computational Chemistry · doi:10.1002/jcc.540100804 · Cited by 2,803
Analytical molecular surface calculation
Connolly, M. L. (1983) · Journal of Applied Crystallography · doi:10.1107/s0021889883010985 · Cited by 2,521
A geometric approach to macromolecule-ligand interactions
Kuntz, I. D., Blaney, J. M., Oatley, S. J., Langridge, R., & Ferrin, T. E. (1982) · Journal of Molecular Biology · doi:10.1016/0022-2836(82)90153-x · Cited by 2,287
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
Jones, G., Willett, P., & Glen, R. C. (1995) · Journal of Molecular Biology · doi:10.1016/s0022-2836(95)80037-9 · Cited by 1,548
Automated docking of substrates to proteins by simulated annealing
Goodsell, D. S., & Olson, A. J. (1990) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340080302 · Cited by 1,315
The development of versions 3 and 4 of the Cambridge Structural Database System
Allen, F. H., Davies, J. E., Galloy, J. J., Johnson, O. W., Kennard, O., Macrae, C. F., Mitchell, E. M., Mitchell, G. F., Smith, J. M., & Watson, D. G. (1991) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00002a004 · Cited by 1,308
Atomic Structures of the Human Immunophilin FKBP-12 Complexes with FK506 and Rapamycin
Duyne, G. D. V., Standaert, R. F., Karplus, P. A., Schreiber, S. L., & Clardy, J. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1012 · Cited by 1,190
Electronegativity. I. Orbital Electronegativity of Neutral Atoms
Hinze, J., & Jaffe, H. H. (1962) · Journal of the American Chemical Society · doi:10.1021/ja00863a008 · Cited by 1,128
Parallel Problem Solving from Nature
(1991) · Lecture notes in computer science · doi:10.1007/bfb0029723 · Cited by 1,049
Quaternary ligand binding to aromatic residues in the active-site gorge of acetylcholinesterase.
Harel, M., Schalk, I. J., Ehret‐Sabatier, L., Bouet, F., Goeldner, M. P., HIRTH, C. G., Axelsen, P. H., Silman, I., & Sussman, J. L. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.19.9031 · Cited by 902
The Nature and Geometry of Intermolecular Interactions between Halogens and Oxygen or Nitrogen
Lommerse, J. P. M., Stone, A. J., Taylor, R., & Allen, F. H. (1996) · Journal of the American Chemical Society · doi:10.1021/ja953281x · Cited by 806
Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., & Kraut, J. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)33497-5 · Cited by 746
Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming
Gehlhaar, D. K., Verkhivker, G. M., Rejto, P. A., Sherman, C. J., Fogel, D. R., Fogel, L. J., & Freer, S. T. (1995) · Chemistry & Biology · doi:10.1016/1074-5521(95)90050-0 · Cited by 684
Distributed Genetic Algorithms
Tanese, R. (1989) · international conference on Genetic algorithms · Cited by 660
Corner flapping: a simple and fast algorithm for exhaustive generation of ring conformations
Goto, M., & O̅sawa, E. (1989) · Journal of the American Chemical Society · doi:10.1021/ja00206a046 · Cited by 475
Structural Aspects of Metal Liganding to Functional Groups in Proteins
GLUSKER, J. P. (1991) · Advances in protein chemistry · doi:10.1016/s0065-3233(08)60534-3 · Cited by 450
A genetic algorithm for flexible molecular overlay and pharmacophore elucidation
Jones, G., Willett, P., & Glen, R. C. (1995) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00124324 · Cited by 392
Computational Methods to Predict Binding Free Energy in Ligand-Receptor Complexes
Murcko, M. A. (1995) · Journal of Medicinal Chemistry · doi:10.1021/jm00026a001 · Cited by 367
Structural factors that control conformational transitions and serotype specificity in type 3 poliovirus.
Filman, D. J., Syed, R., Chow, M., Macadam, A. J., Minor, P. D., & Hogle, J. M. (1989) · The EMBO Journal · doi:10.1002/j.1460-2075.1989.tb03541.x · Cited by 364
Pheromone binding to two rodent urinary proteins revealed by X-ray crystallography
Böcskei, Z., Groom, C. R., Flower, D. R., Wright, C. E., Phillips, S. E. V., Cavaggioni, A., Findlay, J. B. C., & North, A. C. T. (1992) · Nature · doi:10.1038/360186a0 · Cited by 361
An intermolecular perturbation theory for the region of moderate overlap
Hayes, I. C., & Stone, A. J. (1984) · Molecular Physics · doi:10.1080/00268978400102151 · Cited by 281
FLOG: A system to select ?quasi-flexible? ligands complementary to a receptor of known three-dimensional structure
Miller, M. D., Kearsley, S. K., Underwood, D. J., & Sheridan, R. P. (1994) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00119865 · Cited by 281
Flexible ligand docking using a genetic algorithm
Oshiro, C. M., Kuntz, I. D., & Dixon, J. S. (1995) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00124402 · Cited by 275
Refined crystal structures of Escherichia coli and chicken liver dihydrofolate reductase containing bound trimethoprim.
Matthews, D. A., Bolin, J. T., Burridge, J. M., Filman, D. J., Volz, K. W., Kaufman, B. T., Beddell, C. R., Champness, J. N., Stammers, D. K., & Kraut, J. (1985) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)89743-5 · Cited by 271
The Automatic Search for Ligand Binding Sites in Proteins of Known Three-dimensional Structure Using only Geometric Criteria
Peters, K. P., Fauck, J., & Frömmel, C. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0077 · Cited by 248
Conformational changes of small molecules binding to proteins
Nicklaus, M. C., Wang, S., Driscoll, J. S., & Milne, G. W. A. (1995) · Bioorganic & Medicinal Chemistry · doi:10.1016/0968-0896(95)00031-b · Cited by 230
Three‐dimensional structure of a fluorescein–Fab complex crystallized in 2‐methyl‐2,4‐pentanediol
Herron, J. N., He, X., Mason, M. L., Voss, E. W., & Edmundson, A. B. (1989) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340050404 · Cited by 229
Refined crystal structure of β-lactamase from Staphylococcus aureus PC1 at 2.0 Å resolution
Herzberg, O. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90527-d · Cited by 217
Reduced representation model of protein structure prediction: Statistical potential and genetic algorithms
Sun, S. (1993) · Protein Science · doi:10.1002/pro.5560020508 · Cited by 208
THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL 30-->MET VARIANT TO 1.7 ANGSTROMS RESOLUTION
Braden, B. C., Steinrauf, L. K., & Hamilton, J. A. (1993) · Worldwide Protein Data Bank · doi:10.2210/pdb1eta/pdb · Cited by 205
Design, synthesis, and kinetic evaluation of high-affinity FKBP ligands and the X-ray crystal structures of their complexes with FKBP12
Holt, D. A., Luengo, J. I., Yamashita, D. S., Oh, H. J., Konialian-Beck, A. L., Yen, H.-K., Rozamus, L. W., Brandt, M. S., Bossard, M. J., Levy, M. A., et al. (1993) · Journal of the American Chemical Society · doi:10.1021/ja00075a008 · Cited by 201
Refined 2·3ÅX-ray crystal structure of bovine thrombin complexes formed with the benzamidine and arginine-based thrombin inhibitors NAPAP, 4-TAPAP and MQPA
Brandstetter, H., Türk, V., Hoeffken, H. W., Grosse, D., Stürzebecher, J., Martin, P. D., Edwards, B. F. P., & Bode, W. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)91054-s · Cited by 196
Crystal structure of unliganded Escherichia coli dihydrofolate reductase. Ligand-induced conformational changes and cooperativity in binding
Bystroff, C., & Kraut, J. (1991) · Biochemistry · doi:10.1021/bi00222a028 · Cited by 187
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Zhou, G. W., Guo, J., Huang, W., Fletterick, R. J., & Scanlan, T. S. (1994) · Science · doi:10.1126/science.8066444 · Cited by 182
The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30–>Met variant to 1.7-A resolution.
Hamilton, J. A., Steinrauf, L. K., Braden, B. C., Liepnieks, J. J., Benson, M. D., Holmgren, G., Sandgren, O., & Steen, L. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)53792-3 · Cited by 180
Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer
Wang, J., Smerdon, S. J., Jäger, J., Kohlstaedt, L. A., Rice, P. A., Friedman, J. M., & Steitz, T. A. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.15.7242 · Cited by 175
Nuclear magnetic resonance and neutron diffraction studies of the complex of ribonuclease A with uridine vanadate, a transition-state analog
Borah, B., Chen, C. W., Egan, W., Miller, M., Wlodawer, A., & Cohen, J. S. (1985) · Biochemistry · doi:10.1021/bi00329a038 · Cited by 157
DESIGN, SYNTHESIS, AND KINETIC EVALUATION OF HIGH-AFFINITY FKBP LIGANDS, AND THE X-RAY CRYSTAL STRUCTURES OF THEIR COMPLEXES WITH FKBP12
Holt, D. A., Luengo, J. I., Yamashita, D. S., Oh, H.-J., Konialian-Beck, A. L., Yen, H.-K., Rozamus, L. W., Brandt, M. A., Bossard, M. J., Levy, M. A., et al. (1993) · Worldwide Protein Data Bank · doi:10.2210/pdb1fkg/pdb · Cited by 144
Refined crystal structure of type III chloramphenicol acetyltransferase at 1·75 Å resolution
Leslie, A. G. W. (1990) · Journal of Molecular Biology · doi:10.1016/s0022-2836(05)80129-9 · Cited by 141
A good ligand is hard to find: Automated docking methods
Blaney, J. M., & Dixon, J. S. (1993) · Perspectives in Drug Discovery and Design · doi:10.1007/bf02174531 · Cited by 141
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Dreyer, G. B., Lambert, D. M., Meek, T. D., Carr, T. J., Tomaszek, T. A., Fernandez, A. V., BARTUS, H. F., Cacciavillani, E., & Hassell, A. M. (1992) · Biochemistry · doi:10.1021/bi00144a004 · Cited by 128
An Efficient Mean Solvation Force Model for Use in Molecular Dynamics Simulations of Proteins in Aqueous Solution
Fraternali, F., & van Gunsteren, W. F. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0139 · Cited by 126
26-10 Fab-digoxin complex: affinity and specificity due to surface complementarity.
Jeffrey, P. D., Strong, R. K., Sieker, L. C., Chang, C. Y., Campbell, R. L., Petsko, G. A., Haber, E., Margolies, M. N., & Sheriff, S. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.21.10310 · Cited by 122
The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 Å resolution
Diederichs, K., & Schulz, G. E. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)90756-v · Cited by 116
Cavity search: An algorithm for the isolation and display of cavity-like binding regions
Ho, C. M. W., & Marshall, G. R. (1990) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00117400 · Cited by 112
The role of lysine 166 in the mechanism of mandelate racemase from Pseudomonas putida: Mechanistic and crystallographic evidence for stereospecific alkylation by (R)-.alpha.-phenylglycidate
Landro, J. A., Gerlt, J. A., Kozarich, J. W., Koo, C. W., Shah, V. J., Kenyon, G. L., Neidhart, D. J., Fujita, S., & Petsko, G. A. (1994) · Biochemistry · doi:10.1021/bi00169a003 · Cited by 110
Docking small-molecule ligands into active sites
Jones, G., & Willett, P. (1995) · Current Opinion in Biotechnology · doi:10.1016/0958-1669(95)80107-3 · Cited by 103
2·9Åresolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten
Brünger, A. T., Leahy, D. J., Hynes, T. R., & Fox, R. O. (1991) · Journal of Molecular Biology · doi:10.1016/0022-2836(91)80217-i · Cited by 100
Structures of Aromatic Inhibitors of Influenza Virus Neuraminidase
Jedrzejas, M. J., Singh, S., Brouillette, W. J., Laver, W. G., Air, G. M., & Luo, M. (1995) · Biochemistry · doi:10.1021/bi00010a003 · Cited by 98
Sculpting proteins interactively: Continual energy minimization embedded in a graphical modeling system
Surles, M. C., Richardson, J. S., Richardson, D. C., & Brooks, F. P. (1994) · Protein Science · doi:10.1002/pro.5560030205 · Cited by 95
Molecular recognition using a binary genetic search algorithm
Payne, A. W. R., & Glen, R. C. (1993) · Journal of Molecular Graphics · doi:10.1016/0263-7855(93)87001-l · Cited by 94
Crystal Structures of Aconitase with Trans-aconitate and Nitrocitrate Bound
Lauble, H., Kennedy, M. C., Beinert, H., & Stout, C. D. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1246 · Cited by 93
Pharmacophoric pattern matching in files of three-dimensional chemical structures: Comparison of conformational-searching algorithms for flexible searching
Clark, D. E., Jones, G., Willett, P., Kenny, P. W., & Glen, R. C. (1994) · Journal of Chemical Information and Computer Sciences · doi:10.1021/ci00017a026 · Cited by 91
Identifying the Tertiary Fold of Small Proteins with Different Topologies from Sequence and Secondary Structure using the Genetic Algorithm and Extended Criteria Specific for Strand Regions
Dandekar, T., & Argos, P. (1996) · Journal of Molecular Biology · doi:10.1006/jmbi.1996.0115 · Cited by 77
Structure of a Phosphonate-inhibited β-Lactamase
Chen, C. C. H., Rahil, J. F., Pratt, R. F., & Herzberg, O. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1571 · Cited by 75
Application of genetic algorithms in molecular modeling
Brodmeier, T., & Pretsch, E. (1994) · Journal of Computational Chemistry · doi:10.1002/jcc.540150604 · Cited by 71
On the relative strengths of amide…amide and amide…water hydrogen bonds
Mitchell, J. B. O., & Price, S. L. (1991) · Chemical Physics Letters · doi:10.1016/0009-2614(91)85003-f · Cited by 69
On the specificity of antibody/antigen interactions: Phosphocholine binding to McPC603 and the correlation of three-dimensional structure and sequence data
PADLAN, E. A., Cohen, G. H., & Davies, D. R. (1985) · Annales de l Institut Pasteur Immunologie · doi:10.1016/s0769-2625(85)80058-1 · Cited by 66
X-ray Crystallographic Structures of Adipocyte Lipid-Binding Protein Complexed with Palmitate and Hexadecanesulfonic Acid. Properties of Cavity Binding Sites
LaLonde, J. M., Bernlohr, D., & Banaszak, L. J. (1994) · Biochemistry · doi:10.1021/bi00182a017 · Cited by 66
Escherichia coli-derived rat intestinal fatty acid binding protein with bound myristate at 1.5 A resolution and I-FABPArg106—>Gln with bound oleate at 1.74 A resolution.
Eads, J. C., Sacchettini, J. C., Kromminga, A., & Gordon, J. I. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)74325-7 · Cited by 63
A genetic algorithm based method for docking flexible molecules
Judson, R., Jaeger, E. P., & Treasurywala, A. M. (1994) · Journal of Molecular Structure THEOCHEM · doi:10.1016/0166-1280(94)80102-9 · Cited by 63
Crystal structure of inorganic pyrophosphatase from Thermus thermophilus
Teplyakov, A., OBMOLOVA, G., Wilson, K. S., Ishii, K., Kaji, H., Samejima, T., & Kuranova, I. P. (1994) · Protein Science · doi:10.1002/pro.5560030713 · Cited by 60
Docking flexible molecules: A case study of three proteins
Judson, R., Tan, Y. T., Mori, E., Melius, C. F., Jaeger, E. P., Treasurywala, A. M., & Mathiowetz, A. M. (1995) · Journal of Computational Chemistry · doi:10.1002/jcc.540161109 · Cited by 59
The crystal structures at 2.2 angstroms resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
Murthy, K. H. M., Winborne, E., Minnich, M. D., Culp, J. S., & Debouck, C. M. (1992) · Worldwide Protein Data Bank · doi:10.2210/pdb1heg/pdb · Cited by 57
Mechanism of inhibition of 3α,20β-hydroxysteroid dehydrogenaseby a licorice-derived steroidal inhibitor
Ghosh, D., Erman, M., Wawrzak, Z., Duax, W. L., & Pangborn, W. A. (1994) · Structure · doi:10.1016/s0969-2126(94)00099-9 · Cited by 56
Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere
Tong, L., Pav, S., Mui, S., Lamarre, D., Yoakim, C., Beaulieu, P. L., & Anderson, P. C. (1995) · Structure · doi:10.1016/s0969-2126(01)00133-2 · Cited by 54
Structures of thymidylate synthase with a C-terminal deletion: Role of the C-terminus in alignment of 2'-deoxyuridine 5'-monophosphate and 5,10-methylenetetrahydrofolate
Perry, K. M., Carreras, C. W., Chang, L. C., Santi, D. V., & Stroud, R. M. (1993) · Biochemistry · doi:10.1021/bi00079a007 · Cited by 53
Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses
Badger, J., Minor, I., Oliveira, M. A., Smith, T. J., & Rossmann, M. G. (1989) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340060102 · Cited by 53
Principles and pitfalls in designing site‐directed peptide ligands
Edmundson, A. B., Harris, D. L., Fan, Z.-C., Guddat, L. W., Schley, B. T., Hanson, B. L., Tribbick, G., & Geysen, H. M. (1993) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.340160304 · Cited by 50
The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
Murthy, K. H. M., Winborne, E., Minnich, M. D., Culp, J. S., & Debouck, C. M. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)50014-4 · Cited by 50
Structure and activity of two photoreversible cinnamates bound to chymotrypsin
Stoddard, B. L., Bruhnke, J. D., Porter, N. A., Ringe, D., & Petsko, G. A. (1990) · Biochemistry · doi:10.1021/bi00472a017 · Cited by 49
Finding and filling protein cavities using cellular logic operations
Delaney, J. S. (1992) · Journal of Molecular Graphics · doi:10.1016/0263-7855(92)80052-f · Cited by 48
Structure Determination of Antiviral Compound SCH 38057 Complexed with Human Rhinovirus 14
Zhang, A., Nanni, R. G., Li, T., Arnold, G. F., Oren, D. A., Jacobo‐Molina, A., Williams, R. L., Kamer, G., Rubenstein, D. A., Li, Y., et al. (1993) · Journal of Molecular Biology · doi:10.1006/jmbi.1993.1206 · Cited by 43
The structure of a rhombohedral R6 insulin hexamer that binds phenol
Smith, G. D., & Dodson, G. G. (1992) · Biopolymers · doi:10.1002/bip.360320422 · Cited by 39
X-ray crystallographic analysis of inhibition of endothiapepsin by cyclohexyl renin inhibitors
Cooper, J. B., Quail, W., Frazão, C., Foundling, S., Blundell, T. L., Humblet, C. C., Lunney, E. A., Lowther, W. T., & Dunn, B. M. (1992) · Biochemistry · doi:10.1021/bi00150a005 · Cited by 36
Structure of the crystalline complex of cytidylic acid (2'-CMP) with ribonuclease at 1.6 Å resolution. Conservation of solvent sites in RNase-A high-resolution structures
Lisgarten, J. N., Gupta, V., Maes, D., Wyns, L., Zegers, I., Palmer, R. A., Dealwis, C. G., Aguilar, C. F., & Hemmings, A. M. (1993) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s090744499300719x · Cited by 34
Crystal structure of ribonuclease Ms (as a ribonuclease T1 homolog) complexed with a guanylyl-3',5'-cytidine analog
Nonaka, T., Nakamura, K. T., Uesugi, S., Ikehara, M., Masachika, I. R. I. E., & Mitsui, Y. (1993) · Biochemistry · doi:10.1021/bi00095a011 · Cited by 28
A fast empirical method for the calculation of molecular polarizability
Glen, R. C. (1994) · Journal of Computer-Aided Molecular Design · doi:10.1007/bf00125380 · Cited by 27
Correlation of the hydrogen-bond acceptor properties of nitrogen with the geometry of the Nsp 2 →Nsp 3 transition in R 1(X=)C–NR 2 R 3 substructures: reaction pathway for the protonation of nitrogen
Allen, F. H., Bird, C. M., Rowland, R. S., Harris, S. E., & Schwalbe, C. H. (1995) · Acta Crystallographica Section B Structural Science · doi:10.1107/s0108768195004800 · Cited by 21
Mapping common molecular fragments in crystal structures to explore conformation and configuration space under the conditions of a molecular environment
Klebe, G. (1994) · Journal of Molecular Structure THEOCHEM · doi:10.1016/0166-1280(94)80094-4 · Cited by 16

Research works printed but not linked: 2

Dreyer, 1992, Hydroxyethylene isostere inhibitors of human immunodeficiency virus-I protease, Biochemistry, 31
Padlan, 1985, On the specificity of antibody 3-antigen interactions, Ann. Immunol. (Paris), C136, 271

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See all 6,763

Authors: Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R.
Affiliations: University of Sheffield (GB)
Wellcome Trust (GB)
Cambridge Crystallographic Data Centre (GB)
Corresponding author: Jones, Gareth
ORCID: Jones, Gareth
Willett, Peter
Glen, Robert C
Leach, Andrew R
Taylor, Robin
Venue: Journal of Molecular Biology
Publisher: Elsevier BV
Published: 1997-04
Volume: 267
Issue: 3
Pages: 727-748
ISSN: 0022-2836 (ISSN-L)
DOI: 10.1006/jmbi.1996.0897
OpenAlex: W2050456292
Cited by: 6,763
References: 87
Citations by year: 2026: 244 · 2025: 332 · 2024: 356 · 2023: 361 · 2022: 383 · 2021: 414 · 2020: 394 · 2019: 351 · 2018: 327 · 2017: 270 · 2016: 248 · 2015: 234 · 2014: 237 · 2013: 248 · 2012: 274
Type: book review
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
Locations: Journal of Molecular Biology (publishedVersion)
PubMed (publishedVersion)
Topics: Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
Keywords: protein-ligand docking, genetic algorithm, flexible docking, protein-ligand complex, ligand conformational flexibility, rational drug design, binding mode prediction
MeSH terms: Algorithms, Binding Sites, Computer Simulation, Humans, Ligands, Models, Genetic, Models, Molecular, NADP, Protein Binding, Protein Conformation, Proteins, Tetrahydrofolate Dehydrogenase, Crystallography, X-Ray

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Development and validation of a genetic algorithm for flexible docking 1 1Edited by F. E. Cohen

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