TY - BOOK AU - Notling, B. PY - 1993 DA - 1993// TI - Protein Folding Kinetics ID - Notling1993 ER - TY - JOUR AU - Ngo, J. T. AU - Marks, J. AU - Karplus, M. PY - 1992 DA - 1992// TI - Computational Complexity: Protein Structure Prediction and the Levinthal Paradox JO - Protein Engineering VL - 5 UR - https://doi.org/10.1093/protein/5.4.313 DO - 10.1093/protein/5.4.313 ID - Ngo1992 ER - TY - JOUR AU - Unger, R. AU - Moult, J. PY - 1993 DA - 1993// TI - Finding the Lowest Free Energy Conformation of a Protein is a NP-hard Problem: Proof and Implications JO - Bulletin of Mathematical Biology VL - 55 UR - https://doi.org/10.1007/BF02460703 DO - 10.1007/BF02460703 ID - Unger1993 ER - TY - BOOK AU - Hoos, H. H. AU - Stützle, T. PY - 2004 DA - 2004// TI - Stochastic Local Search: Foundations and Applications PB - Morgan Kaufmann Publishers CY - Elsevier ID - Hoos2004 ER - TY - JOUR AU - Bonneau, R. AU - Baker, D. PY - 2001 DA - 2001// TI - Ab Initio Protein Structure Prediction: Progress and Prospects JO - Annual Review of Biophysics and Biomolecular Structure VL - 30 UR - https://doi.org/10.1146/annurev.biophys.30.1.173 DO - 10.1146/annurev.biophys.30.1.173 ID - Bonneau2001 ER - TY - JOUR AU - Kolinski, A. AU - Skolnick, J. PY - 2004 DA - 2004// TI - Reduced Models of Proteins and their Applications JO - Polymer VL - 45 UR - https://doi.org/10.1016/j.polymer.2003.10.064 DO - 10.1016/j.polymer.2003.10.064 ID - Kolinski2004 ER - TY - JOUR AU - Park, B. H. AU - Levitt, M. PY - 1995 DA - 1995// TI - The Complexity and Accuracy of Discrete State Models of Protein Structure JO - Journal of Molecular Biology VL - 249 UR - https://doi.org/10.1006/jmbi.1995.0311 DO - 10.1006/jmbi.1995.0311 ID - Park1995 ER - TY - JOUR AU - Bagci, Z. AU - Jernigan, R. L. AU - Bahar, I. PY - 2002 DA - 2002// TI - Residue coordination in Proteins Conforms to the Closest Packing of Spheres JO - Polymer VL - 43 UR - https://doi.org/10.1016/S0032-3861(01)00427-X DO - 10.1016/S0032-3861(01)00427-X ID - Bagci2002 ER - TY - JOUR AU - Gront, D. AU - Kolinski, A. AU - Skolnick, J. PY - 2000 DA - 2000// TI - Comparison of Three Monte Carlo Conformational Search Strategies for a Protein-like Homopolymer Model: Folding Thermodynamics and Identification of Low-Energy Structures JO - Journal of Chemical Physics VL - 13 UR - https://doi.org/10.1063/1.1289533 DO - 10.1063/1.1289533 ID - Gront2000 ER - TY - JOUR AU - Zhang, Y. AU - Skolnick, J. PY - 2001 DA - 2001// TI - Parallel-Hat Tempering: A Monte Carlo Search Scheme for the Identification of Low-Energy Structures JO - Journal of Chemical Physics VL - 115 UR - https://doi.org/10.1063/1.1396672 DO - 10.1063/1.1396672 ID - Zhang2001 ER - TY - JOUR AU - Pokarowski, P. AU - Kolinski, A. AU - Skolnick, J. PY - 2003 DA - 2003// TI - A Minimal Physically Realistic Protein-Like Lattice Model: Designing and Energy Landscape that Ensures All-Or-None Folding to a Unique Native State JO - Biophysical Journal VL - 84 UR - https://doi.org/10.1016/S0006-3495(03)74964-9 DO - 10.1016/S0006-3495(03)74964-9 ID - Pokarowski2003 ER - TY - JOUR AU - Aloy, P. AU - Stark, A. AU - Hadley, C. AU - Russel, R. B. PY - 2003 DA - 2003// TI - Predictions without Templates: New Folds, Secondary Structure, and Contacts in CASP5 JO - Proteins: Structure, Function, and Genetics VL - 53 UR - https://doi.org/10.1002/prot.10546 DO - 10.1002/prot.10546 ID - Aloy2003 ER - TY - JOUR AU - Jones, D. T. PY - 2001 DA - 2001// TI - Predicting Novel Protein Folds by Using FRAGFOLD JO - Proteins: Structure, Function, and Genetics Suppl VL - 5 UR - https://doi.org/10.1002/prot.1171 DO - 10.1002/prot.1171 ID - Jones2001 ER - TY - JOUR AU - Ortiz, A. R. AU - Kolinski, A. AU - Rotkiewicz, P. AU - Ilkowski, B. AU - Skolnick, J. PY - 1999 DA - 1999// TI - Ab Initio Folding of Proteins Using Restrains Derived from Evolutionary Information JO - Proteins: Structure, Function, and Genetics Suppl VL - 3 UR - https://doi.org/3.0.CO;2-E DO - 3.0.CO;2-E ID - Ortiz1999 ER - TY - JOUR AU - Simons, K. AU - Kooperberg, C. AU - Huang, E. AU - Baker, D. PY - 1997 DA - 1997// TI - Assembly of Protein Tertiary Structures from Fragments with Similar Local Sequences Using Simulated Annealing and Bayesian Scoring Function JO - Journal of Molecular Biology VL - 268 UR - https://doi.org/10.1006/jmbi.1997.0959 DO - 10.1006/jmbi.1997.0959 ID - Simons1997 ER - TY - JOUR AU - Skolnick, J. AU - Kolinski, A. AU - Kihara, D. AU - Betancourt, M. AU - Rotkiewicz, P. AU - Boniecki, M. PY - 2001 DA - 2001// TI - Ab Initio Protein Structure Prediction via a Combination of Threading, Lattice Folding, Clustering, and Structure Refinement JO - Proteins: Structure, Function, and Genetics Suppl VL - 5 UR - https://doi.org/10.1002/prot.1172 DO - 10.1002/prot.1172 ID - Skolnick2001 ER - TY - JOUR AU - Zhang, Y. AU - Kihara, D. AU - Skolnick, J. PY - 2002 DA - 2002// TI - Local Energy Landscape Flattening: Parallel Hyperbolic Monte Carlo Sampling of Protein Folding JO - Proteins: Structure, Function, and Genetics VL - 48 UR - https://doi.org/10.1002/prot.10141 DO - 10.1002/prot.10141 ID - Zhang2002 ER - TY - JOUR AU - Bowie, J. U. AU - Eisenberg, D. PY - 1994 DA - 1994// TI - An Evolutionary Approach to Folding Small α-helical Proteins that Use Sequence Information and an Empirical Guiding Fitness Function JO - Proceedings of the National Academy of Sciences of the USA VL - 91 UR - https://doi.org/10.1073/pnas.91.10.4436 DO - 10.1073/pnas.91.10.4436 ID - Bowie1994 ER - TY - JOUR AU - Dandekar, T. AU - Argos, P. PY - 1994 DA - 1994// TI - Folding the Main Chain of Small Proteins with the Genetic Algorithm JO - Journal of Molecular Biology VL - 236 UR - https://doi.org/10.1006/jmbi.1994.1193 DO - 10.1006/jmbi.1994.1193 ID - Dandekar1994 ER - TY - JOUR AU - Pedersen, J. T. AU - Moult, J. PY - 1997 DA - 1997// TI - Protein Folding Simulations with Genetic Algorithms and a Detailed Molecular Description JO - Journal of Molecular Biology VL - 269 UR - https://doi.org/10.1006/jmbi.1997.1010 DO - 10.1006/jmbi.1997.1010 ID - Pedersen1997 ER - TY - JOUR AU - Hansmann, U. H. E. PY - 1999 DA - 1999// TI - Protein Folding Simulations in a Deformed Energy Landscape JO - The European Physical Journal B VL - 12 UR - https://doi.org/10.1007/s100510051044 DO - 10.1007/s100510051044 ID - Hansmann1999 ER - TY - JOUR AU - Mitsutake, A. AU - Sugita, Y. AU - Okamoto, Y. PY - 2001 DA - 2001// TI - Generalized-Ensemble Algorithms for Molecular Simulations of Biopolymers JO - Biopolymers (Peptide Science) VL - 60 UR - https://doi.org/3.0.CO;2-F DO - 3.0.CO;2-F ID - Mitsutake2001 ER - TY - CHAP AU - Sugita, Y. AU - Okamoto, Y. PY - 2004 DA - 2004// TI - Replica-Exchange Multicanonical Algorithm and Multicanonical Replica-Exchange Method for Simulating Systems with Rough Energy Landscape BT - Condensed Materials Archive ID - Sugita2004 ER - TY - JOUR AU - Okamoto, Y. PY - 2004 DA - 2004// TI - Generalized-Ensemble Algorithms: Enhanced Sampling Techniques for Monte Carlo and Molecular Dynamic Simulations JO - Journal of Molecular Graphics and Modeling VL - 22 UR - https://doi.org/10.1016/j.jmgm.2003.12.009 DO - 10.1016/j.jmgm.2003.12.009 ID - Okamoto2004 ER - TY - JOUR AU - Battiti, R. AU - Tecchiolli, G. PY - 1994 DA - 1994// TI - The Reactive Tabu Search JO - ORSA Journal on Computing VL - 6 UR - https://doi.org/10.1287/ijoc.6.2.126 DO - 10.1287/ijoc.6.2.126 ID - Battiti1994 ER - TY - JOUR AU - Plotkin, S. S. AU - Onuchic, J. N. PY - 2002 DA - 2002// TI - Understanding Protein Folding with Energy Landscape Theory Part I: Basic Concepts JO - Quarterly Reviews of Biophysics VL - 35 ID - Plotkin2002 ER - TY - JOUR AU - Wenzel, W. AU - Hamacher, K. PY - 1999 DA - 1999// TI - Stochastic Tunneling Approach for Global Minimization of Complex Potential Energy Landscapes JO - Physical Review Letters VL - 82 UR - https://doi.org/10.1103/PhysRevLett.82.3003 DO - 10.1103/PhysRevLett.82.3003 ID - Wenzel1999 ER - TY - JOUR AU - Brunette, T. J. AU - Brock, O. PY - 2005 DA - 2005// TI - Improving Protein Structure Prediction with Model-based Search JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti1029 DO - 10.1093/bioinformatics/bti1029 ID - Brunette2005 ER - TY - CHAP AU - Hoos, H. H. AU - Stützle, T. PY - 1998 DA - 1998// TI - On the Empirical Evaluation of Las Vegas Algorithms BT - Proceedings of the 14th Conference on Uncertainty in Artificial Intelligence ID - Hoos1998 ER -