Ab initio modeling of small proteins by iterative TASSER simulations

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dc.contributor.author Wu, Sitao
dc.contributor.author Skolnick, Jeffrey
dc.contributor.author Zhang, Yang
dc.date.accessioned 2009-01-09T19:25:53Z
dc.date.available 2009-01-09T19:25:53Z
dc.date.issued 2007-05-08
dc.identifier.citation BMC Biology 2007, 5:17 en
dc.identifier.issn 1741-7007
dc.identifier.uri http://hdl.handle.net/1853/26289
dc.description © 2007 Wu et al; licensee BioMed Central Ltd.
dc.description The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1741-7007/5/17
dc.description doi:10.1186/1741-7007-5-17
dc.description.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 within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server) in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP)7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.
dc.language.iso en_US en
dc.publisher Georgia Institute of Technology en
dc.subject Protein structure prediction
dc.subject I-TASSER
dc.subject Iterative TASSER simulations
dc.subject High resolution models
dc.title Ab initio modeling of small proteins by iterative TASSER simulations en
dc.type Article en
dc.contributor.corporatename Georgia Institute of Technology. Center for the Study of Systems Biology
dc.contributor.corporatename University of Kansas. Center for Bioinformatics
dc.contributor.corporatename University of Kansas. Dept. of Molecular Biosciences
dc.publisher.original BioMed Central


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