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Home > Research Projects > Algorithmic Theory of Protein Folding

Algorithmic Theory of Protein Folding

Lattice Protein Models Protein Folding Algorithms With Guaranteed Error Bounds Energy Function Inference And Voting Theory Bipole Packing And The Bi-planar Conjecture Of Side Chain Self-assembly Profolding Editors (C++, Mathematica)

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

People: Fumei Lam, Gabriel Negara                               the ProFolding Project Collaborators: Ken Dill (UCSF) Publications: F. Lam and S, Istrail, Combinatorial Algorithms for Protein Folding in Lattice Models: A Survey of Mathematical Results to appear in Communications in Information and Systems Journal  (2009), China 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