TASSER-Lite: an automated tool for protein comparative modeling.
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).
Pandit
Shashi Bhushan
SB
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, GA 30318, USA.
Zhang
Yang
Y
Skolnick
Jeffrey
J
D001331:Automation; D001703:Biophysics / Q000379:methods*; D019295:Computational Biology; D003198:Computer Simulation; D030562:Databases, Protein; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D009010:Monte Carlo Method; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D012984:Software