TASSER-Lite: an automated tool for protein comparative modeling

TitleTASSER-Lite: an automated tool for protein comparative modeling
Publication TypeJournal Article
Year of Publication2006
AuthorsPandit SB, Zhang Y, Skolnick J
JournalBiophys J
Volume91
Issue11
Pagination4180-90
Date Published2006 Dec 1
ISSN0006-3495
KeywordsAutomation, Biophysics, Computational Biology, Computer Simulation, Databases, Protein, Models, Molecular, Models, Statistical, Molecular Conformation, Monte Carlo Method, Protein Conformation, Protein Structure, Tertiary, Proteomics, Software
Abstract

This study involves the development of a rapid comparative modeling tool for homologous sequences by extension of the TASSER methodology, developed for tertiary structure prediction. This comparative modeling procedure was validated on a representative benchmark set of proteins in the Protein Data Bank composed of 901 single domain proteins (41-200 residues) having sequence identities between 35-90% with respect to the template. Using a Monte Carlo search scheme with the length of runs optimized for weakly/nonhomologous proteins, TASSER often provides appreciable improvement in structure quality over the initial template. However, on average, this requires approximately 29 h of CPU time per sequence. Since homologous proteins are unlikely to require the extent of conformational search as weakly/nonhomologous proteins, TASSER's parameters were optimized to reduce the required CPU time to approximately 17 min, while retaining TASSER's ability to improve structure quality. Using this optimized TASSER (TASSER-Lite), we find an average improvement in the aligned region of approximately 10% in root mean-square deviation from native over the initial template. Comparison of TASSER-Lite with the widely used comparative modeling tool MODELLER showed that TASSER-Lite yields final models that are closer to the native. TASSER-Lite is provided on the web at (http://cssb.biology.gatech.edu/skolnick/webservice/tasserlite/index.html).

Alternate JournalBiophysical Journal

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