Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments
暂无分享,去创建一个
[1] David Haussler,et al. Detecting Coevolution in and among Protein Domains , 2007, PLoS Comput. Biol..
[2] Alfonso Valencia,et al. Assessment of intramolecular contact predictions for CASP7 , 2007, Proteins.
[3] B. Rost,et al. Effective use of sequence correlation and conservation in fold recognition. , 1999, Journal of molecular biology.
[4] David K. Y. Chiu,et al. Inferring consensus structure from nucleic acid sequences , 1991, Comput. Appl. Biosci..
[5] C. Yanofsky,et al. Protein Structure Relationships Revealed by Mutational Analysis , 1964, Science.
[6] Robert D. Finn,et al. iPfam: visualization of protein?Cprotein interactions in PDB at domain and amino acid resolutions , 2005, Bioinform..
[7] Gregory B. Gloor,et al. Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction , 2008, Bioinform..
[8] Ramón López de Mántaras,et al. Tractable Bayesian Learning of Tree Augmented Naive Bayes Models , 2003, ICML.
[9] R. Ranganathan,et al. Evolutionarily conserved pathways of energetic connectivity in protein families. , 1999, Science.
[10] D. Baker,et al. A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[11] R. Durbin,et al. RNA sequence analysis using covariance models. , 1994, Nucleic acids research.
[12] Simon A. A. Travers,et al. A Novel Method for Detecting Intramolecular Coevolution: Adding a Further Dimension to Selective Constraints Analyses , 2006, Genetics.
[13] L. Holm,et al. The Pfam protein families database , 2005, Nucleic Acids Res..
[14] W. Fitch,et al. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution , 1970, Biochemical Genetics.
[15] W. Atchley,et al. Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[16] Jesús Cerquides,et al. Tractable Bayesian Learning of Tree Augmented Naive Bayes Classifiers , 2003 .
[17] G. Gloor,et al. Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions. , 2005, Biochemistry.
[18] Richard W Aldrich,et al. On Evolutionary Conservation of Thermodynamic Coupling in Proteins* , 2004, Journal of Biological Chemistry.
[19] W R Taylor,et al. Coevolving protein residues: maximum likelihood identification and relationship to structure. , 1999, Journal of molecular biology.
[20] Tommi S. Jaakkola,et al. Tractable Bayesian learning of tree belief networks , 2000, Stat. Comput..
[21] Pierre Baldi,et al. Improved residue contact prediction using support vector machines and a large feature set , 2007, BMC Bioinformatics.
[22] Sean R. Eddy,et al. Profile hidden Markov models , 1998, Bioinform..
[23] Robert D. Finn,et al. InterPro: the integrative protein signature database , 2008, Nucleic Acids Res..
[24] L. C. Martin,et al. Using information theory to search for co-evolving residues in proteins , 2005, Bioinform..
[25] Kevin Karplus,et al. Contact prediction using mutual information and neural nets , 2007, Proteins.
[26] Najeeb M. Halabi,et al. Protein Sectors: Evolutionary Units of Three-Dimensional Structure , 2009, Cell.
[27] T. Hwa,et al. Identification of direct residue contacts in protein–protein interaction by message passing , 2009, Proceedings of the National Academy of Sciences.
[28] D. Andersson,et al. Adaptation to the deleterious effects of antimicrobial drug resistance mutations by compensatory evolution. , 2004, Research in microbiology.
[29] R. Aldrich,et al. Influence of conservation on calculations of amino acid covariance in multiple sequence alignments , 2004, Proteins.
[30] E. van Nimwegen,et al. Accurate Prediction of Protein–protein Interactions from Sequence Alignments Using a Bayesian Method , 2022 .
[31] Thomas W. H. Lui,et al. Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments , 2003, Bioinform..
[32] David S. Eisenberg,et al. Using inferred residue contacts to distinguish between correct and incorrect protein models , 2008, Bioinform..
[33] Thomas M. Cover,et al. Elements of Information Theory , 2005 .
[34] C. N. Liu,et al. Approximating discrete probability distributions with dependence trees , 1968, IEEE Trans. Inf. Theory.
[35] Alfonso Valencia,et al. Protein co-evolution, co-adaptation and interactions , 2008, The EMBO journal.
[36] Anders Gorm Pedersen,et al. Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation , 2007, Algorithms for molecular biology : AMB.
[37] B. Rost,et al. Conservation and prediction of solvent accessibility in protein families , 1994, Proteins.
[38] Paul P. Gardner,et al. Sequence analysis Measuring covariation in RNA alignments : physical realism improves information measures , 2006 .