NDLI: TASSER-Lite: An Automated Tool for Protein Comparative Modeling

Content Provider	PubMed Central
Author	Pandit, Shashi Bhushan Zhang, Yang Skolnick, Jeffrey
Copyright Year	2006
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 ∼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 ∼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 ∼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.
Related Links	http://dx.doi.org/10.1529/biophysj.106.084293
Ending Page	4190
Page Count	11
Starting Page	4180
File Format	PDF
ISSN	00063495
e-ISSN	15420086
Journal	Biophysical Journal
Issue Number	11
Volume Number	91
Language	English
Publisher	Biophysical Society
Publisher Date	2006-12-01
Access Restriction	Open
Rights Holder	Biophysical Society
Subject Keyword	Biophysics Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Biophysics

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