The particle concept: Placing discrete water molecules during protein- ligand docking predictions

Proteins: Structure, Function and Genetics

Volumn 34, Issue 1, 1999, Pages 17-28

  Rarey, Matthias ^a   Kramer, Bernd ^a   Lengauer, Thomas ^a  

^a FRAUNHOFER INSTITUTE FOR APPLIED INFORMATION TECHNOLOGY FIT   (Germany)

Author keywords

Conformational analysis; Drug design; Flexible docking; Molecular docking; Molecular flexibility; Protein ligand interaction; Water interactions

Indexed keywords

LIGAND; PROTEIN; PROTEINASE; WATER;

ARTICLE; HUMAN IMMUNODEFICIENCY VIRUS 1; HYDROGEN BOND; LIGAND BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING;

ALGORITHMS; ARABINOSE; COMPUTER SIMULATION; DIPEPTIDES; HIV PROTEASE; KINETICS; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; PIPERIDINES; PROTEIN BINDING; TEMPERATURE; THROMBIN; TRYPSINOGEN; WATER;

EID: 0032961895     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19990101)34:1<17::AID-PROT3>3.0.CO;2-1     Document Type: Article

References (22)

1. Andrews PR, Craik DJ, Martin JL. Functional group contributions to drug-receptor interactions. J Med Chem 1984;27:1648-1657.
2. Wlodawer A. Rational drug design: the proteinase inhibitors. Pharmacotherapy 1994;14:9S-20S.
3. Poornima CS, Dean PM. Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. J Comput Aided Mol Des 1995;9:500-512.
4. Levitt M, Park BH. Water: now you see it, now you don't. Structure 1993;15:223-226.
5. Ladbury JE. Just add water! The effect of water on the specificity of protein-ligand binding sites and its potential application to drug design. Chemistry and Biology 1996;3:973-980.
6. Israelachvili J, Wennerström H. Role of hydration and water structure in biological and colloidal interactions. Nature 1996;379: 219-225.
7. Böhm, H-J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J Comput Aided Mol Des 1994;8:243-256.
8. Jain AN. Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J Comput Aided Mol Des 1996;10:427-440.
9. Raymer ML, Sanschagrin PC, Punch WF, Venkataraman S, Goodman ED, Kuhn LA. Predicting conserved water-mediated and polar ligand interactions in proteins using a k-nearest-neighbors genetic algorithm. J Mol Biol 1997;265:445-464
10. Rarey M, Kramer B, Lengauer T, Klebe G. A fast flexible docking method using an incremental construction algorithm. J Mol Biol 1996;261:470-489.
11. Rarey M, Kramer B, Lengauer T. Multiple automatic base selection: protein-ligand docking based on incremental construction without manual intervention. J Comput Aided Mol Des 1997;11: 369-384.
12. Rarey M, Wefing S, Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des 1996;10:41-54.
13. Leach AR, Kuntz ID. Conformational analysis of flexible ligands in macromolecular receptor sites. J Comput Chem 1992;13:730-748.
14. Welch W, Ruppert J, Jain AN. Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. Chemistry and Biology 1996;3:449-462.
15. Makino S, Kuntz ID. Automated flexible ligand docking method and its application for database search. J Comput Chem 1997;18: 1812-1825.
16. Bernstein FC, Koetzle TF, Williams GJB, et al. The protein data bank: A computer based archival file for macromolecular structures. J Mol Biol 1977;112:535-542.
17. Böhm H-J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des 1992;6:61-78.
18. Böhm H-J. LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 1992;6: 593-606.
19. Duda RO, Hart PE. "Pattern Classification and Scene Analysis." New York: John Wiley & Sons, Inc., 1973. 228 p.
20. Kabsch W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr A 1976;32:922-923.
21. Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking. J Mol Biol 1997;267:727-748.
22. Kramer B, Rarey M, Lengauer T. Validation of the FLEXX incremental construction algorithm for protein-ligand docking. Submitted for publication.