High-Throughput parallel blind Virtual Screening using BINDSURF

BMC Bioinformatics

Volumn 13, Issue SUPPL 1, 2012, Pages

  Sánchez Linares, Irene ^a   Pérez Sánchez, Horacio ^a   Cecilia, José M ^a   García, José M ^a  

^a UNIVERSITY OF MURCIA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CLINICAL RESEARCH; DETERMINATION OF PROTEINS; DRUG DISCOVERY; FAST PROCESSING; HIGH-THROUGHPUT; MASSIVELY PARALLELS; PROTEIN SURFACE; VIRTUAL SCREENING;

BINDING SITES; PARALLEL ARCHITECTURES; PROGRAM PROCESSORS; PROTEINS;

LIGANDS;

LIGAND; PROTEIN;

ARTICLE; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPUTER PROGRAM; DRUG DEVELOPMENT; DRUG SCREENING; FACTUAL DATABASE; HUMAN; INSTRUMENTATION; METABOLISM; METHODOLOGY; PROTEIN BINDING;

BINDING SITES; DATABASES, FACTUAL; DRUG DISCOVERY; DRUG EVALUATION, PRECLINICAL; HUMANS; LIGANDS; MODELS, CHEMICAL; PROTEIN BINDING; PROTEINS; SOFTWARE;

EID: 84875064754     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-S14-S13     Document Type: Article

References (35)

1. 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. 10.1093/nar/28.1.235, 102472, 10592235.
2. Sanchez R, Sali A. Large-Scale Protein Structure Modeling of the Saccharomyces cerevisiae Genome. Proc Natl Acad Sci USA 1998, 95(23):13597-13602. 10.1073/pnas.95.23.13597, 24864, 9811845.
3. Garland M, Kirk DB. Understanding throughput-oriented architectures. Commun ACM 2010, 53:58-66.
4. Garland M, Le Grand S, Nickolls J, Anderson J, Hardwick J, Morton S, Phillips E, Zhang Y, Volkov V. Parallel Computing Experiences with CUDA. IEEE Micro 2008, 28:13-27.
5. NVIDIA Whitepaper NVIDIA's Next Generation CUDA Compute Architecture: Fermi 2009, NVIDIA.
6. Pérez-Sánchez H, Wenzel W. Optimization methods for virtual screening on novel computational architectures. Curr Comput Aided Drug Des 2011, 7:44-52. 10.2174/157340911793743565, 20883205.
7. Guerrero G, Pérez-Sánchez H, Wenzel W, Cecilia JM, García JM. Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs. 5th International Conference on Practical Applications of Computational Biology; Bioinformatics (PACBB 2011), Volume 93 2011, 63-69. Springer Berlin/Heidelberg.
8. Sánchez-Linares I, Pérez-Sánchez H, Guerrero GD, Cecilia JM, García JM. Accelerating multiple target drug screening on GPUs. Proceedings of the 9th International Conference on Computational Methods in Systems Biology (CMSB' 11) 2011, 95-102. New York, NY, USA: ACM.
9. Sánchez-Linares I, Pérez-Sánchez H, García JM. Accelerating Grid Kernels for Virtual Screening on Graphics Processing Units. Parallel Computing: Proceedings of the International Conference ParCo 2011, Volume 22 2012, 413-420. D'Hollander E, Padua D, IOS.
10. Brannigan G, LeBard DN, Hénin J, Eckenhoff RG, Klein ML. Multiple binding sites for the general anesthetic isoflurane identified in the nicotinic acetylcholine receptor transmembrane domain. Proc Natl Acad Sci USA 2010, 107(32):14122-14127. 10.1073/pnas.1008534107, 2922517, 20660787.
11. Hetényi C, van der Spoel D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci 2002, 11(7):1729-1737. 2373668, 12070326.
12. Jorgensen W. The many roles of computation in drug discovery. Science 2004, 303(5665):1813-1818. 10.1126/science.1096361, 15031495.
13. Yuriev E, Agostino M, Ramsland PA. Challenges and advances in computational docking: 2009 in review. J Mol Recogn 2011, 24(2):149-164.
14. Huang SY, Zou X. Advances and challenges in protein-ligand docking. Int J Mol Sci 2010, 11(8):3016-3034. 10.3390/ijms11083016, 2996748, 21152288.
15. Morris G, Goodsell D, Halliday R, Huey R, Hart W, Belew R, Olson A. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 1998, 19(14):1639-1662.
16. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004, 47(7):1739-1749. 10.1021/jm0306430, 15027865.
17. Ewing TJA, Makino S, Skillman AG, Kuntz ID. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. J Comput-Aided Mol Des 2001, 15(5):411-428. 10.1023/A:1011115820450, 11394736.
18. Wang R, Lu Y, Fang X, Wang S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J Chem Inform Comput Sci 2004, 44(6):2114-2125.
19. Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E. Equation of State Calculations by Fast Computing Machines. J Chem Phys 1953, 21:1087-1092.
20. Meng E, Shoichet B, Kuntz I. Automated Docking with Grid-Based Energy Evaluation. J Comput Chem 1992, 13(4):505-524.
21. NVIDIA NVIDIA CUDA C Programming Guide 4.0 2011, NVIDIA.
22. Jorgensen W, Maxwell D, TiradoRives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996, 118(45):11225-11236.
23. Schrödinger LLC. The PyMOL Molecular Graphics System, Version 1.3r1 2010,
24. Kokh DB, Wenzel W. Flexible side chain models improve enrichment rates in in silico screening. J Med Chem 2008, 51(19):5919-5931. 10.1021/jm800217k, 18771256.
25. Vidal D, Mestres J. In Silico Receptorome Screening of Antipsychotic Drugs. Mol Inf 2010, 29:543-551.
26. Landon MR, Lieberman RL, Hoang QQ, Ju S, Caaveiro JMM, Orwig SD, Kozakov D, Brenke R, Chuang GY, Beglov D, Vajda S, Petsko GA, Ringe D. Detection of ligand binding hot spots on protein surfaces via fragment-based methods: application to DJ-1 and glucocerebrosidase. J Comput-Aided Mol Des 2009,
27. Ghersi D, Sanchez R. Improving accuracy and efficiency of blind protein-ligand docking by focusing on predicted binding sites. Proteins 2009, 74(2):417-424. 10.1002/prot.22154, 2610246, 18636505.
28. Buch I, Giorgino T, De Fabritiis G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci USA 2011, 108(25):10184-10189. 10.1073/pnas.1103547108, 3121846, 21646537.
29. Dror RO, Pan AC, Arlow DH, Borhani DW, Maragakis P, Shan Y, Xu H, Shaw DE. Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci USA 2011, 108(32):13118-13123. 10.1073/pnas.1104614108, 3156183, 21778406.
30. Shan Y, Kim E, Eastwood MP, Dror RO, Seeliger MA, Shaw DE. How Does a Drug Molecule Find its Target Binding Site?. J Am Chem Soc 2011, 133:9181-9183. 10.1021/ja202726y, 3221467, 21545110.
31. Ghuman J, Zunszain P, Petitpas I, Bhattacharya A, Otagiri M, Curry S. Structural basis of the drug-binding specificity of human serum albumin. J Mol Biol 2005, 353:38-52. 10.1016/j.jmb.2005.07.075, 16169013.
32. Zhang Z, Li Y, Lin B, Schroeder M, Huang B. Identification of cavities on protein surface using multiple computational approaches for drug binding site prediction. Bioinformatics 2011,
33. Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006, 49(23):6789-6801. 10.1021/jm0608356, 3383317, 17154509.
34. Cross JB, Thompson DC, Rai BK, Baber JC, Fan KY, Hu Y, Humblet C. Comparison of Several Molecular Docking Programs: Pose Prediction and Virtual Screening Accuracy. J Chem Inf Model 2009, 49(6):1455-1474. 10.1021/ci900056c, 19476350.
35. Cecilia JM, García JM, Ujaldon M, Nisbet A, Amos M. Parallelization Strategies for Ant Colony Optimisation on GPUs. 14th Int Workshop on Nature Inspired Distributed Computing -NIDISC11- (in conjunction with IPDPS 2011), IEEE 2011, 339-346.