TASSER-Lite: an automated tool for protein comparative modeling.

TASSER-Lite: an automated tool for protein comparative modeling. Research Abstract Details 

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TASSER-Lite: an automated tool for protein comparative modeling. Abstract Text:

Shashi Bhushan Pandit,Yang Zhang,Jeffrey Skolnick,

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).

TASSER-Lite: an automated tool for protein comparative modeling. Publishing Authors By Initials

SB Pandit,Y Zhang,J Skolnick,

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TASSER-Lite: an automated tool for protein comparative modeling. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Biophysical journal

VOLUME: 91

Page Numbers: 4180-90

Journal Abbreviation: Biophys. J.

ISSN: 0006-3495

DAY: 8

MONTH: 09

YEAR: 2006

TASSER-Lite: an automated tool for protein comparative modeling. Information

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LANGUAGE: eng

NlmUniqueID: 370626

TASSER-Lite: an automated tool for protein comparative modeling. Keywords Mesh Terms:

KEYWORDS: Software

MESH TERMS: methods

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Grant and Affiliation Information for TASSER-Lite: an automated tool for protein comparative modeling.

AFFILIATION: Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: GM-48835

ACRONYM: GM

MEDLINETA: Biophys J

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