Populating local minima in the protein conformational space

Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011

Volumn , Issue , 2011, Pages 114-117

  Olson, Brian ^a   Shehu, Amarda ^a,b  

^a Krasnow Institute for Advanced Study   (United States)

^b GEORGE MASON UNIVERSITY   (United States)

Author keywords

fragment based assembly; iterated local search; local minimum; near native conformations; protein native structure

Indexed keywords

CONFORMATIONAL SPACE; GLOBAL MINIMA; ITERATED LOCAL SEARCH; LOCAL MINIMUMS; LOCAL OPTIMA; LOW ENERGIES; LOW-ENERGY CONFORMATIONS; MEMETIC ALGORITHMS; NATIVE STRUCTURES; PROTEIN ENERGY LANDSCAPE; PROTEIN MODELING; PROTEIN STRUCTURE PREDICTION; SEARCH TECHNIQUE; STRUCTURE PREDICTION;

BIOINFORMATICS; CONFORMATIONS; EVOLUTIONARY ALGORITHMS; FORECASTING;

PROTEINS;

EID: 84856024380     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2011.22     Document Type: Conference Paper

References (15)

1. C. B. Anfinsen, "Principles that govern the folding of protein chains," Science, vol. 181, no. 4096, pp. 223-230, 1973.
2. P. Bradley, K. M. S. Misura, and D. Baker, "Toward high-resolution de novo structure prediction for small proteins," Science, vol. 309, no. 5742, pp. 1868-1871, 2005. (Pubitemid 41325099)
3. T. Kortemme and D. Baker, "Computational design of protein-protein interactions," Curr. Opinion Struct. Biol., vol. 8, no. 1, pp. 91-97, 2004.
4. K. A. Dill and H. S. Chan, "From levinthal to pathways to funnels," Nat. Struct. Biol., vol. 4, no. 1, pp. 10-19, 1997.
5. A. Shehu, L. E. Kavraki, and C. Clementi, "Multiscale characterization of protein conformational ensembles," Proteins: Struct. Funct. Bioinf., vol. 76, no. 4, pp. 837-851, 2009.
6. J. DeBartolo, A. Colubri, A. K. Jha, J. E. Fitzgerald, K. F. Freed, and T. R. Sosnick, "Mimicking the folding pathway to improve homology-free protein structure prediction," Proc. Natl. Acad. Sci. USA, vol. 106, no. 10, pp. 3734-3739, 2009.
7. A. Shehu, L. E. Kavraki, and C. Clementi, "Unfolding the fold of cyclic cysteine-rich peptides," Protein Sci., vol. 17, no. 3, pp. 482-493, 2008. (Pubitemid 351281549)
8. B. Olson, K. Molloy, and A. Shehu, "In search of the protein native state with a probabilistic sampling approach," J. Bioinf. and Comp. Biol., vol. 9, no. 3, pp. 383-398, 2011.
9. A. Shehu and B. Olson, "Guiding the search for native-like protein conformations with an ab-initio tree-based exploration," Int. J. Robot. Res., vol. 29, no. 8, pp. 1106-11 227, 2010.
10. S. Luke, Essentials of Metaheuristics. Lulu, 2009, available for free at http://cs.gmu.edu/~sean/book/metaheuristics/.
11. J. Meiler and D. Baker, "Coupled prediction of protein secondary and tertiary structure," Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 21, pp. 12 105-12 110, 2003.
12. B. Olson, K. Molloy, and A. Shehu, "Enhancing sampling of the conformational space near the protein native state," in BIONETICS: Intl. Conf. on Bio-inspired Models of Network, Information, and Computing Systems, Boston, MA, December 2010.
13. A. Shehu, "An ab-initio tree-based exploration to enhance sampling of low-energy protein conformations," Seattle, WA, USA, 2009.
14. M. Islam and M. Chetty, Novel Memetic Algorithm for Protein Structure Prediction, ser. Lecture Notes in Computer Science. Springer Berlin / Heidelberg, 2009, vol. 5866, pp. 412-421.
15. J. Keum, E.S., K. Kim, and E. Santos, "Local minima-based exploration for off-lattice protein folding," in Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE, aug. 2003, pp. 615-616.