Revisiting amino acid substitution matrices for identifying distantly related proteins

Discriminative modelling of context-specific amino acid substitution probabilities

(2012) Christof Angermüller et al.   BIOINFORMATICS

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains

(2012) Tony E. Lewis et al.   NUCLEIC ACIDS RESEARCH

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures

(2012) Ian Sillitoe et al.   NUCLEIC ACIDS RESEARCH

A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships

(2011) Claire Lemaitre et al.   BMC BIOINFORMATICS

Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria

(2011) David Jimenez-Morales et al.   PLoS One

Substitution Matrices of Residue Triplets Derived from Protein Blocks

(2010) Xin Liu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score

(2009) Shashi Pandit et al.   BMC BIOINFORMATICS

Optimizing substitution matrix choice and gap parameters for sequence alignment

(2009) Robert C Edgar   BMC BIOINFORMATICS

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

Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches

(2008) M. M. Lee et al.   BIOINFORMATICS

Searching protein structure databases with DaliLite v.3

(2008) L. Holm et al.   BIOINFORMATICS

A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins

(2008) Kevin Brick et al.   BMC BIOINFORMATICS