Ab initio modeling of small proteins by iterative TASSER simulations
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BioMed Central
Open Access
Research article
Ab initio modeling of small proteins by iterative TASSER simulations Sitao Wu1, Jeffrey Skolnick2 and Yang Zhang*1 Address: 1Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, 2030 Becker Dr, Lawrence, KS 66047, USA and 2Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, 250 14th Street NW, Atlanta, GA 30318, USA Email: Sitao Wu - [email protected]; Jeffrey Skolnick - [email protected]; Yang Zhang* - [email protected] * Corresponding author
Published: 8 May 2007 BMC Biology 2007, 5:17
doi:10.1186/1741-7007-5-17
Received: 9 December 2006 Accepted: 8 May 2007
This article is available from: http://www.biomedcentral.com/1741-7007/5/17 © 2007 Wu et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract Background: Predicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB) library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins. Results: We developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (< 90 residues) were used to generate I-TASSER models, which had an average Cα-root mean square deviation (RMSD) of 3.8Å, with 6 of them having a Cα-RMSD < 2.5Å. The overall result was comparable with the all-atomic ROSETTA simulation, but the central processing unit (CPU) time by I-TASSER was much shorter (150 CPU days vs. 5 CPU hours). Second, data on 20 small proteins (< 120 residues) were used. I-TASSER folded four of them with a Cα-RMSD < 2.5Å. The average Cα-RMSD of the I-TASSER models was 3.9Å, whereas it was 5.9Å using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (< 120 residues) were taken from the PDB library. An average Cα-RMSD of 3.9Å was obtained for the third benchmark, with seven cases having a Cα-RMSD < 2.5Å. Conclusion: Our simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of ITASSER is either much better or is similar wit
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