This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.106.084293v1 91/11/4180    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Pandit, S. B. Articles by Skolnick, J. Search for Related Content PubMed PubMed Citation Articles by Pandit, S. B. Articles by Skolnick, J.

TASSER-Lite: An Automated Tool for Protein Comparative Modeling

Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30318

Correspondence: Address reprint requests to Jeffrey Skolnick, Tel.: 404-407-8976; Fax: 404-385-7478; E-mail: skolnick{at}gatech.edu.

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.

This article has been cited by other articles:

				S. Y. Lee and J. Skolnick Benchmarking of TASSER_2.0: An Improved Protein Structure Prediction Algorithm with More Accurate Predicted Contact Restraints Biophys. J., August 15, 2008; 95(4): 1956 - 1964. [Abstract] [Full Text] [PDF]

				A. Guerler and E.-W. Knapp Novel protein folds and their nonsequential structural analogs Protein Sci., August 1, 2008; 17(8): 1374 - 1382. [Abstract] [Full Text] [PDF]

				H. Zhou and J. Skolnick Ab Initio Protein Structure Prediction Using Chunk-TASSER Biophys. J., September 1, 2007; 93(5): 1510 - 1518. [Abstract] [Full Text] [PDF]