Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. Export

@article{citeulike:388707, abstract = {Point Accepted Mutation (PAM) is the Markov model of amino acid replacements in proteins introduced by Dayhoff and her co-workers (Dayhoff et al., 1978). The PAM matrices and other matrices based on the PAM model have been widely accepted as the standard scoring system of protein sequence similarity in protein sequence alignment tools. Here, we present Contact Accepted mutatiOn (CAO), a Markov model of protein residue contact mutations. The CAO model simulates the interchanging of structurally defined side-chain contacts, and introduces additional structural information into protein sequence alignments. Therefore, similarities between structurally conserved sequences can be detected even without apparent sequence similarity. CAO has been benchmarked on the HOMSTRAD database and a subset of the CATH database, by comparing sequence alignments with reference alignments derived from structural superposition. CAO yields scores that reflect coherently the structural quality of sequence alignments, which has implications particularly for homology modelling and threading techniques.}, address = {Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, NW7 1AA, London, UK. kxlin@nimr.mrc.ac.uk}, author = {Lin, K. and Kleinjung, J. and Taylor, W. R. and Heringa, J.}, citeulike-article-id = {388707}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/12821306}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=12821306}, issn = {1476-9271}, journal = {Comput Biol Chem}, keywords = {alignment, evolution, homology, markov\_model}, month = {May}, number = {2}, pages = {93--102}, posted-at = {2005-11-11 15:51:28}, priority = {2}, title = {Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/12821306}, volume = {27}, year = {2003} }

TY - JOUR ID - citeulike:388707 L3 - citeulike-article-id:388707 N2 - Point Accepted Mutation (PAM) is the Markov model of amino acid replacements in proteins introduced by Dayhoff and her co-workers (Dayhoff et al., 1978). The PAM matrices and other matrices based on the PAM model have been widely accepted as the standard scoring system of protein sequence similarity in protein sequence alignment tools. Here, we present Contact Accepted mutatiOn (CAO), a Markov model of protein residue contact mutations. The CAO model simulates the interchanging of structurally defined side-chain contacts, and introduces additional structural information into protein sequence alignments. Therefore, similarities between structurally conserved sequences can be detected even without apparent sequence similarity. CAO has been benchmarked on the HOMSTRAD database and a subset of the CATH database, by comparing sequence alignments with reference alignments derived from structural superposition. CAO yields scores that reflect coherently the structural quality of sequence alignments, which has implications particularly for homology modelling and threading techniques. IS - 2 JF - Comput Biol Chem SN - 1476-9271 AD - Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, NW7 1AA, London, UK. kxlin@nimr.mrc.ac.uk EP - 102 TI - Testing homology with Contact Accepted mutatiOn (CAO): a contact-based Markov model of protein evolution. VL - 27 SP - 93 KW - alignment KW - evolution KW - homology KW - markov_model AU - Lin, K AU - Kleinjung, J AU - Taylor, WR AU - Heringa, J PY - 2003/05// UR - http://view.ncbi.nlm.nih.gov/pubmed/12821306 ER -