Reliable and robust detection of coevolving protein residues†

Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing

(2012) Thomas A. Hopf et al.   CELL

Protein 3D Structure Computed from Evolutionary Sequence Variation

(2011) Debora S. Marks et al.   PLoS One

Mutual information is critically dependent on prior assumptions: would the correct estimate of mutual information please identify itself?

(2010) Andrew D. Fernandes et al.   BIOINFORMATICS

Linear predictive coding representation of correlated mutation for protein sequence alignment

(2010) Chan-seok Jeong et al.   BMC BIOINFORMATICS

Functionally Compensating Coevolving Positions Are Neither Homoplasic Nor Conserved in Clades

(2010) G. B. Gloor et al.   MOLECULAR BIOLOGY AND EVOLUTION

CDD: a Conserved Domain Database for the functional annotation of proteins

(2010) A. Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Structural and Functional Roles of Coevolved Sites in Proteins

(2010) Saikat Chakrabarti et al.   PLoS One

Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance

(2010) J. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reducing phylogenetic bias in correlated mutation analysis

(2010) Haim Ashkenazy et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Environment-specific amino acid substitution tables: Tertiary templates and prediction of protein folds

(2010) John Overington et al.   PROTEIN SCIENCE

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Correlated Mutations: A Hallmark of Phenotypic Amino Acid Substitutions

(2010) Andreas Kowarsch et al.   PLoS Computational Biology

A new method for revealing correlated mutations under the structural and functional constraints in proteins

(2009) Byung-Chul Lee et al.   BIOINFORMATICS

Correction for phylogeny, small number of observations and data redundancy improves the identification of coevolving amino acid pairs using mutual information

(2009) C. M. Buslje et al.   BIOINFORMATICS

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Identification of Coevolving Residues and Coevolution Potentials Emphasizing Structure, Bond Formation and Catalytic Coordination in Protein Evolution

(2009) Daniel Y. Little et al.   PLoS One

Sequence context-specific profiles for homology searching

(2009) A. Biegert et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of correlated mutations in HIV-1 protease using spectral clustering

(2008) Ying Liu et al.   BIOINFORMATICS

Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics

(2008) J Gregory Caporaso et al.   BMC EVOLUTIONARY BIOLOGY

Rewiring the Specificity of Two-Component Signal Transduction Systems

(2008) Jeffrey M. Skerker et al.   CELL

Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking

(2008) H. Madaoui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analysis of the residue-residue coevolution network and the functionally important residues in proteins

(2008) Byung-Chul Lee et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coevolution in defining the functional specificity

(2008) Saikat Chakrabarti et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Optimal data collection for correlated mutation analysis

(2008) Haim Ashkenazy et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS