A machine learning based approach to improve sidechain optimization

2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011

Volumn , Issue , 2011, Pages 478-480

  Subramaniam, Sabareesh ^a   Natarajan, Sriraam ^b   Senes, Alessandro ^c  

^a University of Wisconsin   (United States)

^b WAKE FOREST UNIVERSITY   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACKBONE STRUCTURES; CONTINUOUS SPACES; FINITE SET; MACHINE LEARNING METHODS; MACHINE-LEARNING; PROTEIN BACKBONE; SIDE-CHAINS; TARGET PROTEINS;

LEARNING SYSTEMS; OPTIMIZATION; PROTEINS;

BIOINFORMATICS;

EID: 84858988079     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2147805.2147875     Document Type: Conference Paper

References (9)

1. Molecular Simulation Library. http://msl-libraries.org.
2. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissig, I. Shindyalov, and P. Bourne. The protein data bank. Nucleic Acids Research, 28:235-242, 2000. (Pubitemid 30047768)
3. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem., 4(2):187-217, Feb 1983.
4. R. F. Goldstein. Efficient rotamer elimination applied to protein side-chains and related spin glasses. Biophys J, 66(5):1335-1340, May 1994. (Pubitemid 24145131)
5. M. Hall, E. Frank, G. Holmes, B. Pfahringer, P.Reutemann, and I. Witten. The weka data mining software: an update. SIGKDD Explor. Newsl., 11:10-18, November 2009.
6. L. Holm and C. Sander. Fast and simple monte carlo algorithm for side chain optimization in proteins: Application to model building by homology. Proteins: Structure, Function, and Bioinformatics, 14(2):213-223, 1992.
7. G. G. Krivov, M. V. Shapovalov, and R. L. Dunbrack. Improved prediction of protein side-chain conformations with SCWRL4. Proteins, 77(4):778-795, Dec. 2009.
8. J. Mendes, C. M. Soares, and M. A. Carrondo. Improvement of side-chain modeling in proteins with the self-consistent mean field theory method based on an analysis of the factors inuencing prediction. Biopolymers, 50(2):111-131, 1999. (Pubitemid 29288162)
9. S. Subramaniam and A. Senes. An energy optimized conformer library for sidechain optimization. In preparation, 2011.