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 Calpha and side-chain based potential consistent with threading based tertiary restraints. Predictions were generated for 745 proteins 201-300 residues in length that cover th...

The recently developed TASSER (Threading/ASSembly/Refinement) method is applied to predict the tertiary structures of all CASP6 targets. TASSER is a hierarchical approach that consists of template identification by the threading program PROSPECTOR_3, followed by tertiary structure assembly via rearranging continuous template fragments. Assembly occurs using parallel hyperbolic Monte Carlo sampl...

We have developed TASSER, a hierarchical approach to protein structure prediction that consists of template identification by threading, followed by tertiary structure assembly via the rearrangement of continuous template fragments guided by an optimized C(alpha) and side-chain-based potential driven by threading-based, predicted tertiary restraints. TASSER was applied to a comprehensive benchm...

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this st...

We develop two complementary pipelines, "Zhang-Server" and "QUARK", based on I-TASSER and QUARK pipelines for template-based modeling (TBM) and free modeling (FM), and test them in the CASP12 experiment. The combination of I-TASSER and QUARK successfully folds three medium-size FM targets that have more than 150 residues, even though the interplay between the two pipelines still awaits further ...

The relative distance and orientation in contacting residue pairs plays a significant role in protein folding and stabilization. We hereby devise a new knowledge-based, coarse-grained contact potential, so-called ICOSA, by correlating inter-residue contact distance and orientation in evaluating pair-wise inter-residue interactions. The rationale of our approach is to establish icosahedral local...

Protein structure prediction approaches usually perform modeling simulations based on reduced representation of protein structures. For biological utilizations, it is an important step to construct full atomic models from the reduced structure decoys. Most of the current full atomic model reconstruction procedures have defects which either could not completely remove the steric clashes among ba...