A new test set for validating predictions of protein-ligand interaction

Proteins: Structure, Function and Genetics

Volumn 49, Issue 4, 2002, Pages 457-471

  Nissink, J Willem M ^a   Murray, Chris ^b   Hartshorn, Mike ^b   Verdonk, Marcel L ^a   Cole, Jason C ^a   Taylor, Robin ^a  

^a CAMBRIDGE CRYSTALLOGRAPHIC DATA CENTRE   (United Kingdom)

^b ASTEX PHARMACEUTICALS   (United Kingdom)

Author keywords

Docking test set; Drug design; Flexible docking; GOLD; Ligand docking; Protein ligand data set; SuperStar; Validation

Indexed keywords

ASPARTIC PROTEINASE; GLYCOSIDASE; HYDROLASE; IMMUNOGLOBULIN; ISOMERASE; LECTIN; LIGAND; LYASE; METALLOPROTEINASE; OXIDOREDUCTASE; PROTEIN; PROTEIN KINASE; SERINE PROTEINASE; TRANSFERASE; VIRUS PROTEIN;

ARTICLE; BINDING SITE; COMPLEX FORMATION; COMPUTER PROGRAM; CRYSTALLOGRAPHY; FILTER; LIGAND BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING;

ALGORITHMS; BINDING SITES; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; INTERNET; LIGANDS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; REPRODUCIBILITY OF RESULTS; RESEARCH DESIGN; SOFTWARE; SOLVENTS; WATER;

EID: 0013133162     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.10232     Document Type: Article

References (34)

1. 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.
2. Kramer B, Rarey M, Lengauer T. Evaluation of the FLexX incremental construction algorithm for protein-ligand docking. Proteins 1999;37:228-241.
3. Pang Y-P, Perola E, Xu K, Prendergast FP. EUDOC: A computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases. J Comp Chem 2001;22:1750-1771.
4. Baxter CA, Murray CW, Waszkowycz B, Jin Li, Sykes RA, Bone RGA, Perkins TDJ, Wylie W, A New approach to molecular docking and its application to virtual screening of chemical databases. J Chem Inf Comput Sci 2000;40:254-262.
5. Ewing TJ, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. J Comput-Aided Mol Design 2001;15:411-428.
6. Taylor JS, Burnett RM. DARWIN: A program for docking flexible molecules. Proteins 2000;41:173-191.
7. Blom NS, Sygusch J. High resolution fast quantitative docking using Fourier domain correlation techniques. Proteins 1997:27:493-506.
8. Liu M, Wang S. MCDOCK: A Monte-Carlo simulation approach to the molecular docking problem, J Comput-Aided Mol Design 1999;13:435-451.
9. Wang J, Kollman PA, Kuntz ID. Flexible ligand docking: A multistep strategy approach. Proteins 1999;36:1-19.
10. Verdonk ML, Cole JC, Taylor R. SuperStar: a knowledge-based approach for identifying interaction sites in proteins. J Mol Biol 1999;289:1093-1108; Verdonk ML, Cole JC, Watson P, Gillet V, Willet P. SuperStar: improved knowledge-based interaction fields for protein binding sites. J Mol Biol 2001;307:841-859; Boer DR, Kroon J, Cole JC, Smith B, Verdonk ML. SuperStar: Comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions. J Mol Biol 2001;312:275-287.
11. Verdonk ML, Cole JC, Taylor R. SuperStar: a knowledge-based approach for identifying interaction sites in proteins. J Mol Biol 1999;289:1093-1108; Verdonk ML, Cole JC, Watson P, Gillet V, Willet P. SuperStar: improved knowledge-based interaction fields for protein binding sites. J Mol Biol 2001;307:841-859; Boer DR, Kroon J, Cole JC, Smith B, Verdonk ML. SuperStar: Comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions. J Mol Biol 2001;312:275-287.
12. Verdonk ML, Cole JC, Taylor R. SuperStar: a knowledge-based approach for identifying interaction sites in proteins. J Mol Biol 1999;289:1093-1108; Verdonk ML, Cole JC, Watson P, Gillet V, Willet P. SuperStar: improved knowledge-based interaction fields for protein binding sites. J Mol Biol 2001;307:841-859; Boer DR, Kroon J, Cole JC, Smith B, Verdonk ML. SuperStar: Comparison of CSD and PDB-based interaction fields as a basis for the prediction of protein-ligand interactions. J Mol Biol 2001;312:275-287.
13. Gohlke H, Hendlich M, Klebe G. Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 2000;295:337-356.
14. Muegge I, Martin YC. A general and fast scoring function for protein-ligand interactions: A simplified potential approach. J Med Chem 1999;42:791-804.
15. Shindyalov IN, Bourne PE. An alternative view of protein fold space, Proteins 2000;38:247-260.
16. Bergner A, Guenther J, Hendlich M, Klebe G, Verdonk ML. Use of Relibase for retrieving complex 3D interaction patterns including crystallographic packing effects, Nucl Acid Res 2002;61:99-110.
17. (a) Sybyl Molecular Modelling Software, Tripos Inc. 1699 South Hanley Rd, Suite 303, St. Louis, MO 63144;
18. (b) Hooft RWW, Sander C, Vriend G. Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures. Proteins 1996;26:363-376.
19. Collaborative Computational Project, Number 4. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst 1994;D50:760- 763.
20. Bruno IJ, Cole JC, Lommerse JPM, Rowland RS, Taylor R, Verdonk ML. IsoStar: A library of information about non-bonded interactions. J Comput-Aided Mol Design 1997;11:525-537.
21. Rowland RS, Taylor R. Intermolecular nonbonded contact distances in organic crystal structures: Comparison with distances expected from van der Waals radii. J Phys Chem 100;1996:7384-7391.
22. Wonnacott TH, Wonnacott RJ. Introductory Statistics, 5th Ed., New York: John Wiley & Sons; 1990.
23. Allen FH, Kennard O. 3D Search and Research Using the Cambridge Structural Database. Chem Design Autom News 1993;8:1, 31-37.
24. Martin JL, Begun J, Schindeler A, Wickramasinghe WA, Alewood D, Alewood PF, Bergman DA, Brinkworth RI, Abbenante G, March DR, Reid RC, Fairlie DP. Molecular recognition of macrocyclic peptidomimetic inhibitors by HIV-1 protease. Biochemistry 1999;38:7978-7988.
25. http://www.ccdc.cam.ac.uk
26. 1ake, 1ctr, 1dbm, 1ela, 1elb, 1eld, 1ele, 1ghb, 1hdy, 1hef, 1icn, 1ivc, 1ivd, 1ive, 1lmo, 1pha, 1ppl, 1stp, 2cgr, 2plv, 3gch, 4fab, 5p2p, 6cpa, 7cpa, 8gch.
27. Viz., 1abe, 1abf, 1aoe, 1apu, 1cbx, 1dbb, 1dbj, 1dmp, 1dog, 1dwb, 1ebg, 1epo, 1etr, 1ets, 1ett, 1fax, 1hpv, 1hsl, 1htf, 1hvr, 1jap, 1mbi, 1okl, 1okm, 1phg, 1ppc, 1pph, 1qbr, 1qbu, 1tlp, 1tmn, 1tng, 1tnh, 1ulb, 1uvs, 1uvt, 2cpp, 2ctc, 2gbp, 2h4n, 2ifb, 2phh, 2tmn, 2tsc, 2ypi, 3tpi, 4dfr, 5abp, 5cpp.
28. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000;28:235-242.
29. Nissink JWM, Verdonk ML, Klebe G. Simple knowledge-based descriptors to predict protein-ligand interactions. Methodology and validation. J Comput-Aided Mol Design 2000;14:787-803.
30. See supplementary material for an overview of distributions of number ofligand atoms, number of rotational bonds and crystallographic resolutions for these sets.
31. These settings are distributed with GOLD Version 1.2, October 2001.
32. See supplementary material for details.
33. Siegel S. Nonparametric Statistics for the Behavioral Sciences. London: McGraw-Hill; 1956.
34. Bondi A. van der Waals volumes and radii. J Phys Chem 1968;68:441-451.