A population-based evolutionary algorithm for sampling minima in the protein energy surface
暂无分享,去创建一个
[1] Amarda Shehu,et al. Guiding the Search for Native-like Protein Conformations with an Ab-initio Tree-based Exploration , 2010, Int. J. Robotics Res..
[2] P. Argos,et al. Potential of genetic algorithms in protein folding and protein engineering simulations. , 1992, Protein engineering.
[3] Amarda Shehu,et al. Guiding Probabilistic Search of the protein conformational Space with Structural Profiles , 2012, J. Bioinform. Comput. Biol..
[4] Eugene Santos,et al. Local minima-based exploration for off-lattice protein folding , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.
[5] Amarda Shehu,et al. In Search of the protein Native State with a Probabilistic Sampling Approach , 2011, J. Bioinform. Comput. Biol..
[6] Amarda Shehu,et al. Conformational Search for the Protein Native State , 2010 .
[7] K. Dill,et al. The Protein Folding Problem , 1993 .
[8] Tanja Kortemme,et al. Computational design of protein-protein interactions. , 2004, Current opinion in chemical biology.
[9] A. Schug,et al. Basin hopping simulations for all-atom protein folding. , 2006, The Journal of chemical physics.
[10] Mark J. Biggs,et al. On Potential Energy Models for EA-based Ab Initio Protein Structure Prediction , 2010, Evolutionary Computation.
[11] J. Doye,et al. Global Optimization by Basin-Hopping and the Lowest Energy Structures of Lennard-Jones Clusters Containing up to 110 Atoms , 1997, cond-mat/9803344.
[12] Andrea Tettamanzi,et al. A Memetic Algorithm for Protein Structure Prediction in a 3D-Lattice HP Model , 2004, EvoWorkshops.
[13] Madhu Chetty,et al. Novel Memetic Algorithm for Protein Structure Prediction , 2009, Australasian Conference on Artificial Intelligence.
[14] N. Metropolis,et al. Equation of State Calculations by Fast Computing Machines , 1953, Resonance.
[15] Ruth Nussinov,et al. fragment folding and assembly Reducing the computational complexity of protein folding via , 2002 .
[16] Amarda Shehu,et al. Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface , 2012, Proteome Science.
[17] J. Onuchic,et al. Theory of Protein Folding This Review Comes from a Themed Issue on Folding and Binding Edited Basic Concepts Perfect Funnel Landscapes and Common Features of Folding Mechanisms , 2022 .
[18] Shuangye Yin,et al. Eris: an automated estimator of protein stability , 2007, Nature Methods.
[19] Michael Wilde,et al. Protein structure prediction enhanced with evolutionary diversity: SPEED , 2010, Protein science : a publication of the Protein Society.
[20] L. Kavraki,et al. Multiscale characterization of protein conformational ensembles , 2009, Proteins.
[21] H. Scheraga,et al. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. , 1987, Proceedings of the National Academy of Sciences of the United States of America.
[22] Richard Bonneau,et al. De novo prediction of three-dimensional structures for major protein families. , 2002, Journal of molecular biology.
[23] D Baker,et al. Global properties of the mapping between local amino acid sequence and local structure in proteins. , 1996, Proceedings of the National Academy of Sciences of the United States of America.
[24] Cecilia Clementi,et al. Unfolding the fold of cyclic cysteine‐rich peptides , 2008, Protein science : a publication of the Protein Society.
[25] James E. Fitzgerald,et al. Mimicking the folding pathway to improve homology-free protein structure prediction , 2009, Proceedings of the National Academy of Sciences.
[26] Dusan P Djurdjevic,et al. Ab initio protein fold prediction using evolutionary algorithms: Influence of design and control parameters on performance , 2006, J. Comput. Chem..
[27] Peter G Wolynes,et al. Protein structure prediction using basin-hopping. , 2008, The Journal of chemical physics.
[28] P. Bradley,et al. Toward High-Resolution de Novo Structure Prediction for Small Proteins , 2005, Science.
[29] P. Wolynes,et al. Water in protein structure prediction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[30] Oliver Brock,et al. Guiding conformation space search with an all‐atom energy potential , 2008, Proteins.
[31] K. Dill,et al. From Levinthal to pathways to funnels , 1997, Nature Structural Biology.
[32] Edmund K. Burke,et al. Multimeme Algorithms for Protein Structure Prediction , 2002, PPSN.
[33] C. Anfinsen. Principles that govern the folding of protein chains. , 1973, Science.
[34] V. Hornak,et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters , 2006, Proteins.
[35] William E. Hart,et al. Robust Proofs of NP-Hardness for Protein Folding: General Lattices and Energy Potentials , 1997, J. Comput. Biol..
[36] Haruki Nakamura,et al. Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.