Optimization of van der waals energy for protein side-chain placement and design

Biophysical Journal

Volumn 101, Issue 7, 2011, Pages 1690-1698

  Fahmy, Amr ^a   Wagner, Gerhard ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN ENGINEERING; ROTATION;

ALGORITHMS; LIGANDS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN ENGINEERING; PROTEINS; ROTATION;

OCTOPUS;

EID: 80053375682     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2011.07.052     Document Type: Article

References (25)

1. N.A. Pierce, and E. Winfree Protein design is NP-hard Protein Eng. 15 2002 779 782 (Pubitemid 36043220)
2. M. Garey, and D. Johnson Computers and Intractability: A Guide to the Theory of NP-Completeness 1979 W. H. Freeman New York
3. J. Desmet, and M. De Maeyer I. Lasters The dead-end elimination theorem and its use in protein side-chain positioning Nature 356 1992 539 542
4. R.F. Goldstein Efficient rotamer elimination applied to protein side-chains and related spin glasses Biophys. J. 66 1994 1335 1340 (Pubitemid 24145131)
5. N. Pierce, and J. Spriet S. Mayo Conformational splitting: a more powerful criterion for dead-end elimination J. Comput. Chem. 21 2000 999 1009
6. D. Gordon, and S. Mayo Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem J. Comput. Chem. 19 1998 1505 1514
7. A.A. Canutescu, A.A. Shelenkov, and R.L. Dunbrack Jr. A graph-theory algorithm for rapid protein side-chain prediction Protein Sci. 12 2003 2001 2014 (Pubitemid 37022822)
8. J. Xu, and B. Berger Fast and accurate algorithms for protein side-chain packing J. Assoc. Comput. Mach. 53 2006 533 557 (Pubitemid 44435051)
9. C. Lee, and S. Subbiah Prediction of protein side-chain conformation by packing optimization J. Mol. Biol. 217 1991 373 388 (Pubitemid 121003947)
10. J.W. Ponder, and F.M. Richards Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes J. Mol. Biol. 193 1987 775 791 (Pubitemid 17020078)
11. R.L. Dunbrack Jr., and M. Karplus Backbone-dependent rotamer library for proteins. Application to side-chain prediction J. Mol. Biol. 230 1993 543 574 (Pubitemid 23161363)
12. S.C. Lovell, and J.M. Word D.C. Richardson The penultimate rotamer library Proteins 40 2000 389 408 (Pubitemid 30624447)
13. R. Bellman Dynamic Programming 1957 Princeton University Press Princeton, NJ
14. G.G. Krivov, M.V. Shapovalov, and R.L. Dunbrack Jr. Improved prediction of protein side-chain conformations with SCWRL4 Proteins 77 2009 778 795
15. M.J. Bower, F.E. Cohen, and R.L. Dunbrack Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool J. Mol. Biol. 267 1997 1268 1282 (Pubitemid 27192637)
16. Z. Xiang, and B. Honig Extending the accuracy limits of prediction for side-chain conformations J. Mol. Biol. 311 2001 421 430 (Pubitemid 32744551)
17. R.L. Dunbrack Jr. Rotamer libraries in the 21st century Curr. Opin. Struct. Biol. 12 2002 431 440
18. N. Pokala, and T.M. Handel Energy functions for protein design: adjustment with protein-protein complex affinities, models for the unfolded state, and negative design of solubility and specificity J. Mol. Biol. 347 2005 203 227 (Pubitemid 40283639)
19. A.D. MacKerell Jr., and B.R. Brooks M. Karplus CHARMM: the energy function and its parameterization with an overview of the program P.v. R. Schleyer, P.R. Schreiner, N.L. Allinger, T. Clark, J. Gasteiger, P. Kollman, H.F. Schaefer III The Encyclopedia of Computational Chemistry Vol. 1 1998 John Wiley London, UK 271-277
20. N. Robertson, and P. Seymour Graph minors. II. Algorithmic aspects of tree-width J. Algorithms 7 1986 309 322
21. M.J. Berardi, and W.M. Shih J.J. Chou Mitochondrial uncoupling protein 2 structure determined by NMR molecular fragment searching Nature 476 2011 109 113
22. D.P. Frueh, and H. Arthanari G. Wagner Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase Nature 454 2008 903 906
23. D. Arnborg, L. Corneil, and A. Proskurowski Complexity of finding embedding in a k-tree SIAM J. Algeb. Disc. Meth. 8 1987 277 284
24. A. Berry, P. Heggerne, and G. Simonet The minimum degree heuristic and the minimal triangulation process Lecture Notes in Computer Science, Springer-Verlag 2880 2003 58 70
25. L.L.C. Schrödinger The PyMOL Molecular Graphics System, V. 1.3r1 2010 Schrödinger New York