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Tertiary Structure Predictions on a Comprehensive Benchmark of Medium to Large Size Proteins

Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York 14203

Correspondence: Address reprint requests to Jeffrey Skolnick, E-mail: skolnick{at}buffalo.edu.

We evaluate tertiary structure predictions on medium to large size proteins by TASSER, a new algorithm that assembles protein structures through rearranging the rigid fragments from threading templates guided by a reduced C and side-chain based potential consistent with threading based tertiary restraints. Predictions were generated for 745 proteins 201–300 residues in length that cover the Protein Data Bank (PDB) at the level of 35% sequence identity. With homologous proteins excluded, in 365 cases, the templates identified by our threading program, PROSPECTOR_3, have a root-mean-square deviation (RMSD) to native < 6.5 Å, with >70% alignment coverage. After TASSER assembly, in 408 cases the best of the top five full-length models has a RMSD < 6.5 Å. Among the 745 targets are 18 membrane proteins, with one-third having a predicted RMSD < 5.5 Å. For all representative proteins less than or equal to 300 residues that have corresponding multiple NMR structures in the Protein Data Bank, 20% of the models generated by TASSER are closer to the NMR structure centroid than the farthest individual NMR model. These results suggest that reasonable structure predictions for nonhomologous large size proteins can be automatically generated on a proteomic scale, and the application of this approach to structural as well as functional genomics represent promising applications of TASSER.

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