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Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition (2004)
| Venue: | Proteins |
| Citations: | 76 - 13 self |
BibTeX
@ARTICLE{Zhou04single-bodyresidue-level,
author = {Hongyi Zhou and Yaoqi Zhou},
title = {Single-body residue-level knowledge-based energy score combined with sequence-profile and secondary structure information for fold recognition},
journal = {Proteins},
year = {2004},
pages = {1005--1013}
}
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Abstract
ergy function is designed for fold recognition. It is a residue-level single-body potential so that highly efficient dynamic programming method can be used for alignment optimization. It contains a backbone torsion term, a buried surface term, and a contact-energy term. The energy score combined with se-quence profile and secondary structure information leads to an algorithm called SPARKS (Sequence, secondary structure Profiles and Residue-level Knowledge-based energy Score) for fold recogni-tion. Compared with the popular PSI-BLAST, SPARKS is 21 % more accurate in sequence-se-quence alignment in ProSup benchmark and 10%, 25%, and 20 % more sensitive in detecting the family, superfamily, fold similarities in the Lindahl bench-mark, respectively. Moreover, it is one of the best methods for sensitivity (the number of correctly recognized proteins), alignment accuracy (based on the MaxSub score), and specificity (the average number of correctly recognized proteins whose scores are higher than the first false positives) in LiveBench 7 among more than twenty servers of non-consensus methods. The simple algorithm used in SPARKS has the potential for further improve-ment. This highly efficient method can be used for fold recognition on genomic scales. A web server is established for academic users on
Keyphrases
fold recognition secondary structure information single-body residue-level knowledge-based energy score maxsub score twenty server residue-level single-body potential energy score non-consensus method fold recogni-tion sequence-se-quence alignment alignment optimization academic user average number alignment accuracy efficient method first false positive ergy function buried surface term backbone torsion term fold similarity web server residue-level knowledge-based energy score popular psi-blast contact-energy term genomic scale prosup benchmark se-quence profile lindahl bench-mark simple algorithm secondary structure profile
