Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites

Proteins: Structure, Function and Bioinformatics

Volumn 74, Issue 2, 2009, Pages 417-424

  Ghersi, Dario ^a   Sanchez, Roberto ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Astex diverse set; Autodock; Binding site discovery; Docking protocol; Reverse virtual screening

Indexed keywords

LIGAND; PROTEIN;

ACCURACY; ALGORITHM; ARTICLE; BINDING AFFINITY; BINDING SITE; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR INTERACTION; PREDICTION; PRIORITY JOURNAL; PROTEIN BINDING; STRUCTURAL GENOMICS; CHEMICAL STRUCTURE; COMPARATIVE STUDY; COMPUTER SIMULATION; EVALUATION; METHODOLOGY; PROTEIN ANALYSIS; PROTEIN DATABASE; SENSITIVITY AND SPECIFICITY;

ALGORITHMS; BINDING SITES; COMPUTER SIMULATION; DATABASES, PROTEIN; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; SENSITIVITY AND SPECIFICITY;

EID: 59449090758     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22154     Document Type: Article

References (15)

1. Hetenyi C, van der Spoel D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci 2002;11:1729-1737.
2. Hetenyi C, van der Spoel D. Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett 2006;580:1447-1450.
3. Paul N, Kellenberger E, Bret G, Muller P, Rognan D. Recovering the true targets of specific ligands by virtual screening of the protein data bank. Proteins Struct Funct Bioinformatics 2004;54:671-680.
4. Brown WM, Vander Jagt DL. Creating artificial binding pocket boundaries to improve the efficiency of flexible ligand binding. J Chem Inf Comput Sci 2004;44:1412-1422.
5. Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998;19:1639-1662.
6. Huey R, Morris GM, Olson AJ, Goodsell DS. A semiempirical free energy force field with charge-based desolvation. J Comput Chem 2007;28:1145-1152.
7. Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, Murray CW. Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 2007;50:726-741.
8. 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.
9. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs. Nucleic Acids Res 1997;25:3389-3402.
10. Laurie ATR, Jackson RM. Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics 2005;21:1908-1916.
11. 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.
12. Ringe D. What makes a binding site a binding site? Curr Opin Struct Biol 1995;5:825-829.
13. de Hoon MJ, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004;20:1453-1454.
14. Ruvinsky AM. Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions. J Comput Chem 2007;28:1364-1372.
15. Lee D, Redfern O, Orengo C. Predicting protein function from sequence and structure. Nat Rev Mol Cell Biol 2007;8:995-1005.