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
Date Published2006 Dec 1
KeywordsAutomation, Biophysics, Computational Biology, Computer Simulation, Databases, Protein, Models, Molecular, Models, Statistical, Molecular Conformation, Monte Carlo Method, Protein Conformation, Protein Structure, Tertiary, Proteomics, Software

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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