Related references
Note: Only part of the references are listed.Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains
Tony E. Lewis et al.
NUCLEIC ACIDS RESEARCH (2013)
New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures
Ian Sillitoe et al.
NUCLEIC ACIDS RESEARCH (2013)
Discriminative modelling of context-specific amino acid substitution probabilities
Christof Angermueller et al.
BIOINFORMATICS (2012)
CD-HIT: accelerated for clustering the next-generation sequencing data
Limin Fu et al.
BIOINFORMATICS (2012)
A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships
Claire Lemaitre et al.
BMC BIOINFORMATICS (2011)
Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria
David Jimenez-Morales et al.
PLOS ONE (2011)
Substitution Matrices of Residue Triplets Derived from Protein Blocks
Xin Liu et al.
JOURNAL OF COMPUTATIONAL BIOLOGY (2010)
Optimizing substitution matrix choice and gap parameters for sequence alignment
Robert C. Edgar
BMC BIOINFORMATICS (2009)
Sequence context-specific profiles for homology searching
A. Biegert et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Simple is beautiful: a straightforward approach to improve the delineation of true and false positives in PSI-BLAST searches
Marianne M. Lee et al.
BIOINFORMATICS (2008)
Searching protein structure databases with DaliLite v.3
L. Holm et al.
BIOINFORMATICS (2008)
A novel series of compositionally biased substitution matrices for comparing Plasmodium proteins
Kevin Brick et al.
BMC BIOINFORMATICS (2008)
Fr-TM-align: a new protein structural alignment method based on fragment alignments and the TM-score
Shashi Bhushan Pandit et al.
BMC BIOINFORMATICS (2008)
Data growth and its impact on the SCOP database: new developments
Antonina Andreeva et al.
NUCLEIC ACIDS RESEARCH (2008)
Optimizing amino acid substitution matrices with a local alignment kernel
Hiroto Saigo et al.
BMC BIOINFORMATICS (2006)
Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions
YM Huang et al.
BIOINFORMATICS (2006)
Pairwise alignment incorporating dipeptide covariation
GE Crooks et al.
BIOINFORMATICS (2005)
Optimizing substitution matrices by separating score distributions
Y Hourai et al.
BIOINFORMATICS (2004)
The ASTRAL Compendium in 2004
JM Chandonia et al.
NUCLEIC ACIDS RESEARCH (2004)
The compositional adjustment of amino acid substitution matrices
YK Yu et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)
Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison
RE Green et al.
PROCEEDINGS OF THE IEEE (2002)
Contextual alignment of biological sequences (Extended abstract)
A Gambin et al.
BIOINFORMATICS (2002)
Optimization of a new score function for the generation of accurate alignments
B Qian et al.
PROTEINS-STRUCTURE FUNCTION AND GENETICS (2002)
rtREV: An amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny
MW Dimmic et al.
JOURNAL OF MOLECULAR EVOLUTION (2002)
Estimating amino acid substitution models: A comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method
T Muller et al.
MOLECULAR BIOLOGY AND EVOLUTION (2002)
Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure
J Gough et al.
JOURNAL OF MOLECULAR BIOLOGY (2001)
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
AA Schäffer et al.
NUCLEIC ACIDS RESEARCH (2001)
Use of residue pairs in protein sequence-sequence and sequence-structure alignments
JS Jung et al.
PROTEIN SCIENCE (2000)
PHAT: a transmembrane-specific substitution matrix
PC Ng et al.
BIOINFORMATICS (2000)