Algorithmic Theory of Protein Folding
Project status: Active
Project Home Page: http://www.cs.brown.edu/people/sorin/lab/pages/proj_atpf.html
People
| Sorin Istrail |
Publications
Caprara, A., Carr, R., Istrail, S., Lancia, G., and Walenz, B. 1001 Optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. Journal of Computational Biology 11, 1 (2004), 27-52. [ pdf ]
Lancia, G., Carr, R., Walenz, B., and Istrail, S. 101 Optimal PDB structure alignments: A branch-and-cut algorithm for the maximum contact map overlap problem. In Proceedings of the 5th Annual Conference on Research in Computational Biology (RECOMB01) (2001), ACM Press, pp. 201-211. [ pdf ]
Schwartz, R., Istrail, S., and King, J. Frequencies of amino-acid strings in globular proteins sequences indicate suppression of blocks of consecutive hydrophobic residues. Protein Science 10 (2001), 1023-1031. [ pdf ]
Goldman, D., Istrail, S., and Papadimitriou, C. Algorithms aspects of protein structure similarity. In Proceedings of the 40th Annual IEEE Symposium on the Foundations of Computer Science (FOCS99) (Oct. 1999), IEEE Computer Society Press. [ pdf ]
Istrail, S., Schwartz, R., and King, J. Lattice simulations of aggregation funnels of protein folding. Journal of Computational Biology 6, 2 (1999).
Hart, W. E., and Istrail, S. Lattice and off-lattice side chain models of protein folding: linear time structure prediction better than 86 percent of optimal (extended abstract). In Proceedings of the 1st Annual Conference on Research in Computational Biology (RECOMB97) (Jan. 1997), ACM Press, pp. 137-146. [ pdf ]
Hart, W. E., and Istrail, S. Robust proofs of NP-hardness for protein folding: general lattices and energy potentials. Journal of Computational Biology 4, 1 (1997), 1-22.
Hart, W. E., and Istrail, S. Invariant patterns in crystal lattices: implications for protein folding algorithms. In Proceedings of the 7th Conference on Combinatorial Pattern Matching (CPM96) (June 1996), Springer (Lecture Notes in Computer Science), pp. 288-303. [ pdf ]
Hart, W. E., and Istrail, S. Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal (extended abstract). Journal of Computational Biology 3, 1 (1996), 53-96.
Hart, W. E., and Istrail, S. Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal (extended abstract). In Proceedings of the 27nd ACM Symposium on the Theory of Computing (STOC95) (1995), ACM Press, pp. 157-168. [ pdf ]
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