Template-based modeling and free modeling by I-TASSER in CASP7

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Abstract
We developed and tested the I-TASSER protein structure prediction algorithm in the CASP7 experiment, where targets are first threaded through the PDB library and continuous fragments in the threading alignments are exploited to assemble the global structure. The final models are obtained from the progressive refinements started from the last round structure clusters. A majority of the targets in the template-based modeling (TBM) category have the templates drawn closer to the native structure by more than 1 Å within the aligned regions. For the free-modeling (FM) targets, I-TASSER builds correct topology for 7/19 cases with sequence up to 155 residues long. For the first time, the automated server prediction generates models as good as the human-expert does in all the categories, which shows the robustness of the method and the potential of the application to genome-wide structure prediction. Despite the success, the accuracy of I-TASSER modeling is still dominated by the similarity of the template and target structures with a strong correlation coefficient (∼0.9) between the root-mean-squared deviation (RMSD) to native of the templates and the final models. Especially, there is no high-resolution model below 2 Å for the FM targets. These problems highlight the issues that need to be addressed in the next generation of atomic-level I-TASSER development especially for the FM target modeling. Proteins 2007.