A phylogenetic mixture model for the identification of functionally divergent protein residues

Identification of subfamily-specific sites based on active sites modeling and clustering

(2010) Raquel C. de Melo-Minardi et al.   BIOINFORMATICS

Active site prediction using evolutionary and structural information

(2010) Sriram Sankararaman et al.   BIOINFORMATICS

Multi-Harmony: detecting functional specificity from sequence alignment

(2010) B. W. Brandt et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Ensemble approach to predict specificity determinants: benchmarking and validation

(2009) Saikat Chakrabarti et al.   BMC BIOINFORMATICS

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Biological Sequence Simulation for Testing Complex Evolutionary Hypotheses: indel-Seq-Gen Version 2.0

(2009) Cory L. Strope et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Predicting Protein Ligand Binding Sites by Combining Evolutionary Sequence Conservation and 3D Structure

(2009) John A. Capra et al.   PLoS Computational Biology

Characterization and prediction of residues determining protein functional specificity

(2008) John A. Capra et al.   BIOINFORMATICS

Prediction of specificity-determining residues for small-molecule kinase inhibitors

(2008) Daniel R Caffrey et al.   BMC BIOINFORMATICS

A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

(2008) Huai-Chun Wang et al.   BMC EVOLUTIONARY BIOLOGY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Rapid comparison of properties on protein surface

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