A Constraint-Based Approach to Structure Prediction for Simplified Protein Models That Outperforms Other Existing Methods
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[1] M. Karplus,et al. Kinetics of protein folding. A lattice model study of the requirements for folding to the native state. , 1994, Journal of molecular biology.
[2] Mihalis Yannakakis,et al. On the complexity of protein folding (abstract) , 1998, RECOMB '98.
[3] Steven Skiena,et al. Local Rules for Protein Folding on a Triangular Lattice and Generalized Hydrophobicity in the HP Model , 1997, J. Comput. Biol..
[4] Toby Walsh,et al. Principles and Practice of Constraint Programming — CP 2001: 7th International Conference, CP 2001 Paphos, Cyprus, November 26 – December 1, 2001 Proceedings , 2001, Lecture Notes in Computer Science.
[5] Erich Bornberg-Bauer,et al. Chain growth algorithms for HP-type lattice proteins , 1997, RECOMB '97.
[6] William E. Hart,et al. Lattice and Off-Lattice Side Chain Models of Protein Folding: Linear Time Structure Prediction Better than 86% of Optimal , 1997, J. Comput. Biol..
[7] K. Dill,et al. Cooperativity in protein-folding kinetics. , 1993, Proceedings of the National Academy of Sciences of the United States of America.
[8] M Karplus,et al. The folding mechanism of larger model proteins: role of native structure. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[9] R Samudrala,et al. Ab initio construction of protein tertiary structures using a hierarchical approach. , 2000, Journal of molecular biology.
[10] Rolf Backofen,et al. Fast, Constraint-Based Threading of HP-Sequences to Hydrophobic Cores , 2001, CP.
[11] Rolf Backofen,et al. Optimally Compact Finite Sphere Packings - Hydrophobic Cores in the FCC , 2001, CPM.
[12] Sebastian Will. Constraint-Based Hydrophobic Core Construction for Protein Structure Prediction in the Face-Centered-Cubic Lattice , 2002, Pacific Symposium on Biocomputing.
[13] Yue,et al. Sequence-structure relationships in proteins and copolymers. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.
[14] Rolf Backofen,et al. Application of constraint programming techniques for structure prediction of lattice proteins with extended alphabets , 1999, Bioinform..
[15] Rolf Backofen,et al. Algorithmic approach to quantifying the hydrophobic force contribution in protein folding , 1999, German Conference on Bioinformatics.
[16] Eugene I. Shakhnovich,et al. Enumeration of all compact conformations of copolymers with random sequence of links , 1990 .
[17] M. Levitt,et al. The complexity and accuracy of discrete state models of protein structure. , 1995, Journal of molecular biology.
[18] William E. Hart,et al. Fast Protein Folding in the Hydrophobic-Hydrophillic Model within Three-Eights of Optimal , 1996, J. Comput. Biol..
[19] J Moult,et al. Local interactions dominate folding in a simple protein model. , 1996, Journal of molecular biology.
[20] E I Shakhnovich,et al. Impact of local and non-local interactions on thermodynamics and kinetics of protein folding. , 1995, Journal of molecular biology.
[21] J. Skolnick,et al. Combined multiple sequence reduced protein model approach to predict the tertiary structure of small proteins. , 1998, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[22] Erich Bornberg-Bauer,et al. Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[23] Gert Smolka. The Oz Programming Model , 1996 .
[24] Rolf Backofen. An Upper Bound for Number of Contacts in the HP-Model on the Face-Centered-Cubic Lattice (FCC) , 2000, CPM.
[25] R. Jernigan,et al. Residue coordination in proteins conforms to the closest packing of spheres , 2002 .
[26] Hue Sun Chan,et al. History-dependent phenomena in the transverse Ising ferroglass: The free-energy landscape , 2000 .
[27] D. Yee,et al. Principles of protein folding — A perspective from simple exact models , 1995, Protein science : a publication of the Protein Society.
[28] Joxan Jaffar,et al. Principles and Practice of Constraint Programming – CP’99 , 1999, Lecture Notes in Computer Science.
[29] K. Dill,et al. A lattice statistical mechanics model of the conformational and sequence spaces of proteins , 1989 .
[30] Jan van Leeuwen,et al. Computer Science Today , 1995, Lecture Notes in Computer Science.
[31] Agostino Dovier,et al. Using Secondary Structure Information for Protein Folding in CLP(FD) , 2002, Electron. Notes Theor. Comput. Sci..
[32] Frank Thomson Leighton,et al. Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.
[33] Frank Thomson Leighton,et al. Protein folding in the hydrophobic-hydrophilic (HP) is NP-complete , 1998, RECOMB '98.
[34] R A Goldstein,et al. The foldability landscape of model proteins , 1997, Biopolymers.
[35] Barry Cipra,et al. Packing Challenge Mastered At Last , 1998, Science.
[36] E. Bornberg-Bauer,et al. Modeling evolutionary landscapes: mutational stability, topology, and superfunnels in sequence space. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[37] Rolf Backofen,et al. Excluding Symmetries in Constraint-Based Search , 1999, Constraints.
[38] K Yue,et al. Forces of tertiary structural organization in globular proteins. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[39] M Levitt,et al. From structure to sequence and back again. , 1996, Journal of molecular biology.
[40] R. Jernigan,et al. Residue packing in proteins: Uniform distribution on a coarse-grained scale , 2002 .
[41] Anthony J. Guttmann,et al. Self-avoiding walks on the simple cubic lattice , 2000 .
[42] N. Madras,et al. THE SELF-AVOIDING WALK , 2006 .
[43] Eugene C. Freuder. A Sufficient Condition for Backtrack-Free Search , 1982, JACM.
[44] E I Shakhnovich,et al. A test of lattice protein folding algorithms. , 1995, Proceedings of the National Academy of Sciences of the United States of America.
[45] Rolf Backofen. The Protein Structure Prediction Problem: A Constraint Optimization Approach using a New Lower Bound , 2004, Constraints.
[46] Mihalis Yannakakis,et al. On the Complexity of Protein Folding , 1998, J. Comput. Biol..
[47] Neil J. A. Sloane,et al. Kepler's conjecture confirmed , 1998, Nature.
[48] Michael Levitt,et al. A brighter future for protein structure prediction , 1999, Nature Structural Biology.