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Comparison of sequence and structure alignments for protein domains
Author(s) -
MarchlerBauer Aron,
Panchenko Anna R.,
Ariel Naomi,
Bryant Stephen H.
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10163
Subject(s) - protein superfamily , structural alignment , sequence (biology) , computational biology , sequence alignment , domain (mathematical analysis) , similarity (geometry) , protein sequencing , protein domain , protein structure , structural similarity , multiple sequence alignment , identification (biology) , computer science , loop modeling , bioinformatics , biology , protein structure prediction , genetics , peptide sequence , artificial intelligence , mathematics , gene , mathematical analysis , biochemistry , botany , image (mathematics)
Profile search methods based on protein domain alignments have proven to be useful tools in comparative sequence analysis. Domain alignments used by currently available search methods have been computed by sequence comparison. With the growth of the protein structure database, however, alignments of many domain pairs have also been computed by structure comparison. Here, we examine the extent to which information from these two sources agrees. We measure agreement with respect to identification of homologous regions in each protein, that is, with respect to the location of domain boundaries. We also measure agreement with respect to identification of homologous residue sites by comparing alignments and assessing the accuracy of the molecular models they predict. We find that domain alignments in publicly available collections based on sequence and structure comparison are largely consistent. However, the homologous regions identified by sequence comparison are often shorter than those identified by 3D structure comparison. In addition, when overall sequence similarity is low alignments from sequence comparison produce less accurate molecular models, suggesting that they less accurately identify homologous sites. These observations suggest that structure comparison results might be used to improve the overall accuracy of domain alignment collections and the performance of profile search methods based on them. Proteins 2002;48:439–446. © 2002 Wiley‐Liss, Inc.