Application of the docking program SOL for CSAR benchmark

Journal of Chemical Information and Modeling

Volumn 53, Issue 8, 2013, Pages 1946-1956

  Sulimov, Alexey V ^a,b   Kutov, Danil C ^a   Oferkin, Igor V ^a,b   Katkova, Ekaterina V ^a,b   Sulimov, Vladimir B ^a,b  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b Engineering and Consulting Center On Rotordynamics Alfa Tranzit Co   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

APPLICATION PROGRAMS; BENCHMARKING; BINDING ENERGY; FREE ENERGY; GENETIC ALGORITHMS; LIGANDS; MOLECULAR MODELING; PROGRAM PROCESSORS; PROTEINS; SOFTWARE TESTING; STRAIN ENERGY; VAN DER WAALS FORCES;

DOCKING PROGRAMS; INHIBITION ACTIVITY; INTERNAL STRAINS; MULTI-PROCESSORS; POST PROCESSING; PROTEIN LIGANDS; SIMPLE LINEAR REGRESSION; TARGET PROTEINS;

SOLS;

LIGAND;

AREA UNDER THE CURVE; ARTICLE; DRUG DATABASE; MOLECULAR DOCKING; QUALITY CONTROL; STRUCTURE ACTIVITY RELATION;

AREA UNDER CURVE; BENCHMARKING; DATABASES, PHARMACEUTICAL; LIGANDS; MOLECULAR DOCKING SIMULATION; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84883237038     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400094h     Document Type: Article

References (29)

1. Kitchen, D. B.; Decornez, H.; Furr, J. R.; Bajorath, J. Docking and scoring in virtual screening for drug discovery: methods and applications Nat. Rev. Drug Discovery 2004, 3, 935-949
2. Zoete, V.; Grosdidier, A.; Michielin, O. Docking, virtual high throughput screening and in silico fragment-based drug design J. Cell. Mol. Med. 2009, 13, 238-248
3. Gastreich, M.; Lemmen, C.; Briem, H.; Rarey, M. In Virtual Screening in Drug Discovery; Alvarez, J.; Shoichet, B., Eds.; CRC Press: Boca Raton, FL, 2005; pp 25-46.
4. Cole, J. C.; Nissink, J. W. M.; Taylor, R. In Virtual Screening in Drug Discovery; Alvarez, J.; Shoichet, B., Eds.; CRC Press: Boca Raton, FL, 2005; pp 379-415.
5. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function J. Comput. Chem. 1998, 19, 1639-1662
6. Morris, G. M.; Huey, R.; Lindstrom, W.; Sanner, M. F.; Belew, R. K.; Goodsell, D. S.; Olson, A. J. AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility J. Comput. Chem. 2009, 30, 2785-2791
7. Sousa, S. F.; Fernandes, P. A.; Ramos, M. J. Protein-ligand docking: Current status and future challenges Proteins 2006, 65, 15-26
8. Romanov, A. N.; Kondakova, O. A.; Grigoriev, F. V.; Sulimov, A. V.; Luschekina, S. V.; Martynov, Ya.B.; Sulimov, V. B. The SOL docking package for computer-aided drug design Numer. Methods Program. 2008, 9 (2) 64-84, (in Russian)
9. Halgren, T. A. Merck molecular force field J. Comput. Chem. 1996, 17 (5&6) 490-641
10. Ghosh, A.; Rapp, C. S.; Friesner, R. A. Generalized Born model based on a surface integral formulation J. Phys. Chem. B 1998, 102, 10983-10990
11. Romanov, A. N.; Jabin, S. N.; Martynov, Y. B.; Sulimov, A. V.; Grigoriev, F. V.; Sulimov, V. B. surface generalized Born method: A simple, fast and precise implicit solvent model beyond the Coulomb approximation J. Phys. Chem. A 2004, 108, 9323-9327
12. The validation of SOL docking program. http://www.keenbase.ru/en/index. htm (accessed June 21, 2013).
13. Protein Data Bank. http://www.rcsb.org/ (accessed June 21, 2013).
14. Moscow University Supercomputing Center. http://hpc.msu.ru/ (accessed June 21, 2013).
15. Sinauridze, E. I.; Romanov, A. N.; Gribkova, I. V.; Kondakova, O. A.; Surov, S. S.; Gorbatenko, A. S.; Butylin, A. A.; Monakov, M. Y.; Bogolubov, A. A.; Kuznetsov, Y. V.; Sulimov, V. B.; Ataullakhanov, F. I. New synthetic thrombin inhibitors: Molecular design and experimental verification PLoS One 2011, 6 (5) e19969 10.1371/journal.pone.0019969
16. Oferkin, I. V.; Sulimov, A. V.; Kondakova, O. A.; Sulimov, V. B. Implementation of parallel computing for docking programs SOLGRID and SOL Numer. Methods Program. 2011, 12 (1) 205-219, (in Russian)
17. Nocedal, J.; Wright, S. J. Numerical Optimization, 2nd ed.; Springer Science+Business Media, LLC: New York, 2006; section 7.2.
18. Kupervasser, O. Y.; Zhabin, S. N.; Martynov, Y. B.; Fedulov, K. M.; Oferkin, I. V.; Sulimov, A. V.; Sulimov, V. B. Continual model of solvent: The DISOLV software-Algorithms, implementation, and validation Numer. Methods Program. 2011, 12, 246-261, (in Russian)
19. Sulimov, V. B.; Katkova, E. V.; Oferkin, I. V.; Kochugaeva, M. P. PCM, COSMO, and Surface GB Implementation in Program DISOLV: Development and Validation, 244th ACS National Meeting, Philadelphia, Pennsylvania, August 19-23, 2012, oral presentation COMP 441.
20. Zhabin, S. N.; Sulimov, V. B. Construction of the adaptively triangulated smooth molecular surface: Program TAGSS Sci. Visualization 2011, 3 (2) 27-53
21. Connolly, M. L. Solvent-accessible surfaces of proteins and nucleic acids Science 1983, 221 (4612) 709-713
22. Vorobjev, Y. N.; Hermans, J. SIMS: computation of a smooth invariant molecular surface Biophys. J. 1997, 73, 722-732
23. Bordner, A. J.; Cavasotto, C. N.; Abagyan, R. A. Accurate transferable model for water, n-octanol, and n-hexadecane solvation free energies J. Phys. Chem. B. 2002, 106, 11009-11015
24. Bohm, 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. Design 1994, 8, 243-256
25. Schwartzl, S. M.; Tschopp, T. B.; Smith, J. C.; Fischer, S. Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction? J. Comput. Chem. 2002, 23, 1143-1149
26. ChemAxon. http://www.chemaxon.com/ (accessed June 21, 2013).
27. Open Babel: The Open Source Chemistry Toolbox. http://openbabel.org/ (accessed June 21, 2013).
28. Sulimov, A. V.; Kutov, D. K.; Katkova, E. V.; Sulimov, V. B. In Application of the Docking Program SOL for CSAR Benchmark, 244th ACS National Meeting, Philadelphia, Pennsylvania, August 19-23, 2012, oral presentation COMP 48.
29. Chang, C. A.; Chen, W.; Gilson, M. K. Ligand configurational entropy and protein binding Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 1534-1539