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ALGORITHMIC
THEORY
OF
PROTEIN
FOLDING
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Brown University
Department of
Computer Science
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< Sorin Istrail's Homepage :: Research Interests
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ALGORITHMIC THEORY OF PROTEIN FOLDING
Research themes:
- Lattice Protein Folding Algorithms
with mathematically guaranteed Error Bound
- Graph Theory of Self avoiding Walks
- Contact Maps and Protein Structure
- Energy Function Inference pb
- PDB Structure Alignment
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People: Fumei Lam, Gabriel Negara
the ProFolding Project
Collaborators: Ken Dill (UCSF)
Publications:
- A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz,
1001 Optimal PDB Structure Alignments: Integer Programming
Methods for Finding the Maximum Contact Map Overlap},
Journal of Computational Biology, vol 11, No. 1, pp 27-52, 2004
- G. Lancia, R. Carr, B. Walenz, S. Istrail, 101 Optimal PDB Structure Alignments: A Branch-and-Cut Algorithm
for the Maximum Contact Map Overlap Problem, Proceeding
of the Fifth International Conference on Research on Computational Biology, (RECOMB01),
ACM Press, p. 201-211, 2001
- W. E. Hart, S. Istrail, Invariant Patterns in Crystal
Lattices: Implications for Protein Folding Algorithms,
Proceedings of the 7th Conference on Combinatorial Pattern Matching (CPM96),
Springer Lecture Notes in Computer Science, pp. 288-303, June 1996
- W. E. Hart, S. Istrail,
Fast Protein Folding in the Hydrophobic-Hydrophilic Model Within Three-eighths of
Optimal (Extended Abstract), Proceedings of 27th Annual
ACM Symposium on Theory of Computation (STOC95), ACM Press, pp. 157-168,
1995
- D. Goldman, S. Istrail, C. Papadimitriou,
Algorithmic Aspects of Protein Structure Similarity,
Proceedings of the IEEE Symposium on Foundations of Computer
Science (FOCS99), IEEE Computer Society Press, October 1999
- W. E. Hart, S. Istrail,
Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure
Prediction Better than 86\% of Optimal (Extended Abstract),
First International Conference on Computational Molecular Biology, (RECOMB97),
ACM Press, January 20-23, pp. 137-146, 1997
- A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz,
1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the
Maximum Contact Map Overlap}, Journal of Computational Biology, vol 11, No. 1, pp
27-52, 2004
- R. Schwartz, R., S. Istrail, J. King, Frequencies of amino-acid
strings in globular proteins sequences indicate suppression of blocks of consecutive
hydrophobic residues, Protein Science 10:
1023-1031, 2001
- S. Istrail, R. Schwartz, J. King, Lattice Simulations
of Aggregation Funnels of Protein Folding, Journal of
Computational Biology, vol. 6, no. 2, 1999
- W. E. Hart, S. Istrail, Robust Proofs of NP-Hardness for
Protein Folding: General Lattices and Energy Potentials,
Journal of Computational Biology, Vol. 4, No. 1, pp. 1-22, 1997
- W. E. Hart, S. Istrail, Fast Protein Folding in the Hydrophobic-Hydrophilic
Model Within Three-eighths of Optimal, Journal of Computational
Biology, Vol. 3, Number 1, pp. 53-96, 1996
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