We developed BSP-SLIM, a new method for ligand-protein blind docking using low-resolution protein structures. For a given sequence, protein structures are first predicted by I-TASSER; putative ligand binding sites are transferred from holo-template structures which are analogous to the I-TASSER models; ligand-protein docking conformations are then constructed by shape and chemical match of liga...

I-TASSER is an automated pipeline for protein tertiary structure prediction using multiple threading alignments and iterative structure assembly simulations. In CASP9 experiments, two new algorithms, QUARK and fragment-guided molecular dynamics (FG-MD), were added to the I-TASSER pipeline for improving the structural modeling accuracy. QUARK is a de novo structure prediction algorithm used for ...

Molecular replacement (MR) is one of the most common techniques used for solving the phase problem in X-ray crystal diffraction. The success rate of MR however drops quickly when the sequence identity between query and templates is reduced, while the I-TASSER-MR server is designed to solve the phase problem for proteins that lack close homologous templates. Starting from a sequence, it first ge...

To improve the accuracy of TASSER models especially in the limit where threading provided template alignments are of poor quality, we have developed the TASSER algorithm which uses the templates and contact restraints from TASSER generated models for iterative structure refinement. We apply TASSER to a large benchmark set of 2,773 nonhomologous single domain proteins that are 200 in length and ...

Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with suffic...

The post-genomic era has witnessed an explosion of protein sequences in the public databases; but this has not been complemented by the availability of genome-wide structure and function information, due to the technical difficulties and labor expenses incurred by existing experimental techniques. The rapid advancements in computer-based protein structure prediction methods have enabled automat...

We have developed an ab initio protein structure prediction method called chunk-TASSER that uses ab initio folded supersecondary structure chunks of a given target as well as threading templates for obtaining contact potentials and distance restraints. The predicted chunks, selected on the basis of a new fragment comparison method, are folded by a fragment insertion method. Full-length models a...

An automated protein structure prediction algorithm, pro-sp3-Threading/ASSEmbly/Refinement (TASSER), is described and benchmarked. Structural templates are identified using five different scoring functions derived from the previously developed threading methods PROSPECTOR_3 and SP(3). Top templates identified by each scoring function are combined to derive contact and distant restraints for sub...

The TASSER structure prediction algorithm is employed to investigate whether NMR structures can be moved closer to their corresponding X-ray counterparts by automatic refinement procedures. The benchmark protein dataset includes 61 nonhomologous proteins whose structures have been determined by both NMR and X-ray experiments. Interestingly, by starting from NMR structures, the majority (79%) of...