Mapping Monomeric Threading to Protein–Protein Structure Prediction

Mapping Monomeric Threading to Protein-Protein Structure Prediction

The key step of template-based protein-protein structure prediction is the recognition of complexes from experimental structure libraries that have similar quaternary fold. Maintaining two monomer and dimer structure libraries is however laborious, and inappropriate library construction can degrade template recognition coverage. We propose a novel strategy SPRING to identify complexes by mappin...

The Threading Approach to Tertiary Structure Prediction

The threading and sequence-structure alignment approachs are based on the observation that many protein structures in the PDB are very similar. For example, there are many 4-helical bundles, TIM barrels, globins, etc. in the set of solved structures. As a result of this, many scientists have conjectured there are only a limited number of “unique” protein folds in nature. Estimates vary consider...

Structure Prediction by Protein Threading

The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on “the inverse protein folding problem” laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet p...

LOMETS: A local meta-threading-server for protein structure prediction

We developed LOMETS, a local threading meta-server, for quick and automated predictions of protein tertiary structures and spatial constraints. Nine state-of-the-art threading programs are installed and run in a local computer cluster, which ensure the quick generation of initial threading alignments compared with traditional remote-server-based meta-servers. Consensus models are generated from...

Protein structure prediction by threading : force field philosophy ,