A Data-Driven Evolutionary Algorithm for Mapping Multibasin Protein Energy Landscapes
暂无分享,去创建一个
[1] K. Dill,et al. From Levinthal to pathways to funnels , 1997, Nature Structural Biology.
[2] J Günter Grossmann,et al. Dimer destabilization in superoxide dismutase may result in disease-causing properties: structures of motor neuron disease mutants. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[3] Jack Dongarra,et al. LAPACK: a portable linear algebra library for high-performance computers , 1990, SC.
[4] A. Fernández-Medarde,et al. Ras in cancer and developmental diseases. , 2011, Genes & cancer.
[5] Claudio Soto,et al. Protein misfolding and neurodegeneration. , 2008, Archives of neurology.
[6] Amarda Shehu,et al. Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface , 2012, Proteome Science.
[7] J. Onuchic,et al. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations , 2006, Proceedings of the National Academy of Sciences.
[8] Stewart A. Adcock,et al. Molecular dynamics: survey of methods for simulating the activity of proteins. , 2006, Chemical reviews.
[9] R. Nussinov,et al. The role of dynamic conformational ensembles in biomolecular recognition. , 2009, Nature chemical biology.
[10] Ole J Mengshoel,et al. The Crowding Approach to Niching in Genetic Algorithms , 2008, Evolutionary Computation.
[11] Joelle N Pelletier,et al. Protein motions promote catalysis. , 2004, Chemistry & biology.
[12] Samuel L. DeLuca,et al. Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You , 2010, Biochemistry.
[13] Michele Vendruscolo,et al. Dynamic Visions of Enzymatic Reactions , 2006, Science.
[14] D. Kern,et al. The role of dynamics in allosteric regulation. , 2003, Current opinion in structural biology.
[15] A. D. McLachlan,et al. A mathematical procedure for superimposing atomic coordinates of proteins , 1972 .
[16] Elizabeth J. Denning,et al. Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions. , 2009, Journal of molecular biology.
[17] Brian S. Olson,et al. Multi-Objective Optimization Techniques for Conformational Sampling in Template-Free Protein Structure Prediction , 2014 .
[18] John A Tainer,et al. ALS mutants of human superoxide dismutase form fibrous aggregates via framework destabilization. , 2003, Journal of molecular biology.
[19] Claudio Soto,et al. Unfolding the role of protein misfolding in neurodegenerative diseases , 2003, Nature Reviews Neuroscience.
[20] Michele Magrane,et al. UniProt Knowledgebase: a hub of integrated protein data , 2011, Database J. Biol. Databases Curation.
[21] L. Kavraki,et al. Multiscale characterization of protein conformational ensembles , 2009, Proteins.
[22] Haruki Nakamura,et al. Announcing the worldwide Protein Data Bank , 2003, Nature Structural Biology.
[23] Mitsuhiko Ikura,et al. Structural basis for simultaneous binding of two carboxy-terminal peptides of plant glutamate decarboxylase to calmodulin. , 2003, Journal of molecular biology.
[24] R. Conwit,et al. Preventing familial ALS: A clinical trial may be feasible but is an efficacy trial warranted? , 2006, Journal of the Neurological Sciences.
[25] Michael A Hough,et al. The structure of holo and metal-deficient wild-type human Cu, Zn superoxide dismutase and its relevance to familial amyotrophic lateral sclerosis. , 2003, Journal of molecular biology.
[26] D. Kern,et al. Dynamic personalities of proteins , 2007, Nature.
[27] D. Borchelt,et al. Variation in the biochemical/biophysical properties of mutant superoxide dismutase 1 enzymes and the rate of disease progression in familial amyotrophic lateral sclerosis kindreds. , 1999, Human molecular genetics.
[28] Qiang Lu,et al. Single molecule conformational dynamics of adenylate kinase: energy landscape, structural correlations, and transition state ensembles. , 2008, Journal of the American Chemical Society.
[29] Yaohang Li,et al. Pareto-Based Optimal Sampling Method and Its Applications in Protein Structural Conformation Sampling , 2013 .
[30] Lydia E. Kavraki,et al. Understanding Protein Flexibility through Dimensionality Reduction , 2003, J. Comput. Biol..
[31] L. Kay,et al. Intrinsic dynamics of an enzyme underlies catalysis , 2005, Nature.
[32] Colin R. Reeves,et al. Evolutionary computation: a unified approach , 2007, Genetic Programming and Evolvable Machines.
[33] J. Onuchic,et al. Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.
[34] Dominik Gront,et al. Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates , 2007, J. Comput. Chem..
[35] Yaohang Li,et al. Improving predicted protein loop structure ranking using a Pareto-optimality consensus method , 2010, BMC Structural Biology.
[36] Amarda Shehu,et al. Efficient basin hopping in the protein energy surface , 2012, 2012 IEEE International Conference on Bioinformatics and Biomedicine.
[37] Amarda Shehu,et al. Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface , 2013, BCB.