The Statistical Mechanics Approach to Protein Sequence Data: Beyond Contact Prediction
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[1] K. Katoh,et al. MAFFT version 5: improvement in accuracy of multiple sequence alignment , 2005, Nucleic acids research.
[2] George A. Khoury,et al. Protein folding and de novo protein design for biotechnological applications. , 2014, Trends in biotechnology.
[3] Thomas A. Hopf,et al. Protein 3D Structure Computed from Evolutionary Sequence Variation , 2011, PloS one.
[4] Maurice G. Kendall,et al. The advanced theory of statistics , 1945 .
[5] W. S. Valdar,et al. Scoring residue conservation , 2002, Proteins.
[6] W. P. Russ,et al. Evolutionary information for specifying a protein fold , 2005, Nature.
[7] Thomas A. Hopf,et al. Sequence co-evolution gives 3D contacts and structures of protein complexes , 2014, eLife.
[8] P. Bork,et al. Predicting biological networks from genomic data , 2008, FEBS letters.
[9] Ann M Stock,et al. Two-component signal transduction. , 2000, Annual review of biochemistry.
[10] R. Huber,et al. Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II. , 1984, Journal of molecular biology.
[11] Michael T. Laub,et al. Pervasive degeneracy and epistasis in a protein-protein interface , 2015, Science.
[12] C. Sander,et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families , 2011, Proceedings of the National Academy of Sciences.
[13] Gary D Bader,et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry , 2002, Nature.
[14] W. P. Russ,et al. Natural-like function in artificial WW domains , 2005, Nature.
[15] B. Lunt,et al. Dissecting the Specificity of Protein-Protein Interaction in Bacterial Two-Component Signaling: Orphans and Crosstalks , 2011, PloS one.
[16] A. Valencia,et al. Computational methods for the prediction of protein interactions. , 2002, Current opinion in structural biology.
[17] R. Ozawa,et al. A comprehensive two-hybrid analysis to explore the yeast protein interactome , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[18] Terence Hwa,et al. High-resolution protein complexes from integrating genomic information with molecular simulation , 2009, Proceedings of the National Academy of Sciences.
[19] C. Sander,et al. Correlated mutations and residue contacts in proteins , 1994, Proteins.
[20] T. Hwa,et al. Identification of direct residue contacts in protein–protein interaction by message passing , 2009, Proceedings of the National Academy of Sciences.
[21] I. Schlichting,et al. Crystal Structures of a New Class of Allosteric Effectors Complexed to Tryptophan Synthase* , 2002, The Journal of Biological Chemistry.
[22] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[23] A. Valencia,et al. High-confidence prediction of global interactomes based on genome-wide coevolutionary networks , 2008, Proceedings of the National Academy of Sciences.
[24] Tony Pawson,et al. WW Domains Provide a Platform for the Assembly of Multiprotein Networks , 2005, Molecular and Cellular Biology.
[25] David E. Kim,et al. Full title Improved de novo Structure Prediction in CASP 11 by Incorporating Co-evolution Information into Rosetta Short title Structure Prediction using Co-evolution , 2015 .
[26] Thomas A. Hopf,et al. Protein structure prediction from sequence variation , 2012, Nature Biotechnology.
[27] Graham J. G. Upton,et al. A Dictionary of Statistics , 2002 .
[28] Junmei Wang,et al. Development and testing of a general amber force field , 2004, J. Comput. Chem..
[29] David J. C. MacKay,et al. Information Theory, Inference, and Learning Algorithms , 2004, IEEE Transactions on Information Theory.
[30] M Vendruscolo,et al. Recovery of protein structure from contact maps. , 1997, Folding & design.
[31] David Haussler,et al. Detecting Coevolution in and among Protein Domains , 2007, PLoS Comput. Biol..
[32] Thomas A. Hopf,et al. Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing , 2012, Cell.
[33] A. Valencia,et al. From residue coevolution to protein conformational ensembles and functional dynamics , 2015, Proceedings of the National Academy of Sciences.
[34] Benoit H. Dessailly,et al. Exploring the structure and function paradigm. , 2008, Current opinion in structural biology.
[35] Anton J. Enright,et al. Myriads of protein families, and still counting , 2003, Genome Biology.
[36] D. Eisenberg,et al. Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[37] S. Stenholm. Information, Physics and Computation, by Marc Mézard and Andrea Montanari , 2010 .
[38] D. Baker,et al. Robust and accurate prediction of residue–residue interactions across protein interfaces using evolutionary information , 2014, eLife.
[39] Michael J. Mossinghoff,et al. Combinatorics and graph theory , 2000 .
[40] Peter E. Latham,et al. Pairwise Maximum Entropy Models for Studying Large Biological Systems: When They Can Work and When They Can't , 2008, PLoS Comput. Biol..
[41] A. Valencia,et al. In silico two‐hybrid system for the selection of physically interacting protein pairs , 2002, Proteins.
[42] E. Marcotte,et al. Predicting functional linkages from gene fusions with confidence. , 2002, Applied bioinformatics.
[43] A. Lehninger. Principles of Biochemistry , 1984 .
[44] Judea Pearl,et al. Probabilistic reasoning in intelligent systems - networks of plausible inference , 1991, Morgan Kaufmann series in representation and reasoning.
[45] K. Katoh,et al. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.
[46] J. Onuchic,et al. An all‐atom structure‐based potential for proteins: Bridging minimal models with all‐atom empirical forcefields , 2009, Proteins.
[47] A. Tramontano,et al. New encouraging developments in contact prediction: Assessment of the CASP11 results , 2016, Proteins.
[48] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[49] R. Baierlein. Probability Theory: The Logic of Science , 2004 .
[50] R. Bauerle,et al. The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications. , 1999, Proceedings of the National Academy of Sciences of the United States of America.
[51] Massimiliano Pontil,et al. PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments , 2012, Bioinform..
[52] Marcin J. Skwark,et al. Improved Contact Predictions Using the Recognition of Protein Like Contact Patterns , 2014, PLoS Comput. Biol..
[53] M Wilmanns,et al. Three-dimensional structure of the bifunctional enzyme phosphoribosylanthranilate isomerase: indoleglycerolphosphate synthase from Escherichia coli refined at 2.0 A resolution. , 1992, Journal of molecular biology.
[54] Tommi S. Jaakkola,et al. Tractable Bayesian learning of tree belief networks , 2000, Stat. Comput..
[55] Robert D. Finn,et al. The Pfam protein families database , 2004, Nucleic Acids Res..
[56] Nigel F. Delaney,et al. Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins , 2006, Science.
[57] C. Sander,et al. Predicting the functional impact of protein mutations: application to cancer genomics , 2011, Nucleic acids research.
[58] E. Jaynes. Information Theory and Statistical Mechanics , 1957 .
[59] F. Y. Wu. The Potts model , 1982 .
[60] David T. Jones,et al. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins , 2014, Bioinform..