Structural informatics, modeling, and design with an open-source Molecular Software Library (MSL)

Journal of Computational Chemistry

Volumn 33, Issue 20, 2012, Pages 1645-1661

  Kulp, Daniel W ^a   Subramaniam, Sabareesh ^b   Donald, Jason E ^c   Hannigan, Brett T ^d   Mueller, Benjamin K ^b   Grigoryan, Gevorg ^e   Senes, Alessandro ^b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c Agrivida Inc   (United States)

^d UNIVERSITY OF PENNSYLVANIA   (United States)

^e DARTMOUTH COLLEGE   (United States)

Author keywords

conformer library; docking; molecular modeling; protein design; rotamer library; side chain optimization; structure prediction

Indexed keywords

ATOMIC COORDINATE; C++ LIBRARIES; COMMON PLATFORM; COMPLEX APPLICATIONS; DESIGN PROJECTS; ENERGY FUNCTIONS; GEOMETRIC TRANSFORMATIONS; INFORMATICS; LINES OF CODE; MODELING TASK; MOLECULAR ALGORITHM; OPEN-SOURCE; OPEN-SOURCE SOFTWARES; PROTEIN DESIGN; PROTEIN MODELING; RE-UTILIZATION; ROTAMERS; SIDE-CHAINS; SOFTWARE LIBRARIES; SOLVENT ACCESSIBLE SURFACE AREAS; STRUCTURE PREDICTION; UNIQUE FEATURES;

ALGORITHMS; AMINO ACIDS; DESIGN; DOCKING; MATHEMATICAL TRANSFORMATIONS; MOLECULAR MODELING; STRUCTURAL OPTIMIZATION;

COMPUTER SOFTWARE;

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN DATABASE; THERMODYNAMICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 84862572941     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.22968     Document Type: Article

References (49)

1. R. Nair, J. Liu, T.-T. Soong, T. B. Acton, J. K. Everett, A. Kouranov, A. Fiser, A. Godzik, L. Jaroszewski, C. Orengo, G. T. Montelione, B. Rost, J. Struct. Funct. Genomics 2009, 10, 181.
2. Y. Zhang, Curr. Opin. Struct. Biol. 2008, 18, 342.
3. M. I. Sadowski, D. T. Jones, Curr. Opin. Struct. Biol. 2009, 19, 357.
4. E. Verschueren, P. Vanhee, A. M. van der Sloot, L. Serrano, F. Rousseau, J. Schymkowitz, Curr. Opin. Struct. Biol. 2011, 21, 452.
5. Y. Shen, R. Vernon, D. Baker, A. Bax, J. Biomol. NMR 2009, 43, 63.
6. G. Ghirlanda, Curr. Opin. Chem. Biol. 2009, 13, 643.
7. A. Elofsson, G. von Heijne, Annu. Rev. Biochem. 2007, 76, 125.
8. A. Senes, Curr. Opin. Struct. Biol. 2011, 21, 460.
9. R. J. Pantazes, M. J. Grisewood, C. D. Maranas, Curr. Opin. Struct. Biol. 2011, 21, 467.
10. C. Floudas, H. Fung, S. McAllister, M. Monnigmann, R. Rajgaria, Chem. Eng. Sci. 2006, 61, 966.
11. S. M. Lippow, B. Tidor, Curr. Opin. Biotechnol. 2007, 18, 305.
12. J. E. Stajich, D. Block, K. Boulez, S. E. Brenner, S. A. Chervitz, C. Dagdigian, G. Fuellen, J. G. R. Gilbert, I. Korf, H. Lapp, H. Lehväslaiho, C. Matsalla, C. J. Mungall, B. I. Osborne, M. R. Pocock, P. Schattner, M. Senger, L. D. Stein, E. Stupka, M. D. Wilkinson, E. Birney, Genome Res. 2002, 12, 1611.
13. P. J. A. Cock, T. Antao, J. T. Chang, B. A. Chapman, C. J. Cox, A. Dalke, I. Friedberg, T. Hamelryck, F. Kauff, B. Wilczynski, M. J. L. de Hoon, Bioinformatics 2009, 25, 1422.
14. B. W. Berger, D. W. Kulp, L. M. Span, J. L. DeGrado, P. C. Billings, A. Senes, J. S. Bennett, W. F. DeGrado, Proc. Natl. Acad. Sci. USA 2010, 107, 703.
15. Y. Zhang, D. W. Kulp, J. D. Lear, W. F. DeGrado, J. Am. Chem. Soc. 2009, 131, 11341.
16. I. V. Korendovych, A. Senes, Y. H. Kim, J. D. Lear, H. C. Fry, M. J. Therien, J. K. Blasie, F. A. Walker, W. F. Degrado, J. Am. Chem. Soc. 2010, 132, 15516.
17. J. E. Donald, Y. Zhang, G. Fiorin, V. Carnevale, D. R. Slochower, F. Gai, M. L. Klein, W. F. Degrado, Proc. Natl. Acad. Sci. USA 2011, 108, 3958.
18. I. V. Korendovych, D. W. Kulp, Y. Wu, H. Cheng, H. Roder, W. F. Degrado, Proc. Natl. Acad. Sci. USA 2011, 132, 15516.
19. J. E. Donald, D. W. Kulp, W. F. DeGrado, Proteins 2011, 79, 898.
20. A. Senes, D. C. Chadi, P. B. Law, R. F. S. Walters, V. Nanda, W. F. Degrado, J. Mol. Biol. 2007, 366, 436.
21. S. Subramaniam, A. Senes, (submitted for publication).
22. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne, Nucleic Acids Res. 2000, 28, 235.
23. Stepanov, Alexander, Lee, Meng, HP Laboratories Technical Report 95-11(R.1), 1995.
24. W. DeLano, PyMOL Molecular Graphics System, 2002.
25. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, J. Comput. Chem. 1983, 4, 187.
26. R. L. Dunbrack, F. E. Cohen, Protein Sci. 1997, 6, 1661.
27. R. P. Shetty, P. I. W. De Bakker, M. A. DePristo, T. L. Blundell, Protein Eng. 2003, 16, 963.
28. Z. Xiang, B. Honig, J. Mol. Biol. 2001, 311, 421.
29. T. Lazaridis, M. Karplus, Proteins 1999, 35, 133.
30. T. Lazaridis, Proteins 2003, 52, 176.
31. G. G. Krivov, M. V. Shapovalov, R. L. Dunbrack, Proteins 2009, 77, 778.
32. C. Zhang, S. Liu, H. Zhou, Y. Zhou, Protein Sci. 2004, 13, 400.
33. J. Desmet, M. D. Maeyer, B. Hazes, I. Lasters, Nature 1992, 356, 539.
34. P. Koehl, M. Delarue, J. Mol. Biol. 1994, 239, 249.
35. C. A. Voigt, D. B. Gordon, S. L. Mayo, J. Mol. Biol. 2000, 299, 789.
36. C. L. Kingsford, B. Chazelle, M. Singh, Bioinformatics 2005, 21, 1028.
37. B. Gough, GNU Scientific Library Reference Manual, 3rd ed., Network Theory Ltd., 2009.
38. C. J. A. Sigrist, L. Cerutti, E. de Castro, P. S. Langendijk-Genevaux, V. Bulliard, A. Bairoch, N. Hulo, Nucleic Acids Res. 2010, 38, D161.
39. A. Senes, M. Gerstein, D. M. Engelman, J. Mol. Biol. 2000, 296, 921.
40. W. P. Russ, D. M. Engelman, J. Mol. Biol. 2000, 296, 911.
41. D. J. Mandell, T. Kortemme, Nat. Chem. Biol. 2009, 5, 797.
42. A. A. Canutescu, A. A. Shelenkov, R. L. Dunbrack, Protein Sci. 2003, 12, 2001.
43. I. Georgiev, D. Keedy, J. S. Richardson, D. C. Richardson, B. R. Donald, Bioinformatics 2008, 24, i196.
44. D. Gront, D. W. Kulp, R. M. Vernon, C. E. M. Strauss, D. Baker, PLoS One 2011, 6; DOI 10.1371/journal.pone.0023294.
45. D. Gront, S. Kmiecik, A. Kolinski, J. Comput. Chem. 2007, 28, 1593.
46. C. A. Rohl, C. E. M. Strauss, K. M. S. Misura, D. Baker, Methods Enzymol. 2004, 383, 66.
47. C. A. Smith, T. Kortemme, PLoS One 2011, 6, e20451.
48. R. Ihaka, R. Gentleman, J. Comput. Graphical Stat. 1996, 5, 299.
49. A. B. Chowdry, K. A. Reynolds, M. S. Hanes, M. Voorhies, N. Pokala, T. M. Handel, J. Comput. Chem. 2007, 28, 2378.