Parallel-ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites

Parallel-ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites

The ProBiS algorithm performs a local structural comparison of the query protein surface against the nonredundant database of protein structures. It finds proteins that have binding sites in common with the query protein. Here, we present a new parallelized algorithm, Parallel-ProBiS, for detecting similar binding sites on clusters of computers. The obtained speedups of the parallel ProBiS scal...

ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

MOTIVATION Exploitation of locally similar 3D patterns of physicochemical properties on the surface of a protein for detection of binding sites that may lack sequence and global structural conservation. RESULTS An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a databa...

A Fast Algorithm for Protein Structural Comparison

The goal of protein structural comparison attempts to establish an equivalence relation between polymer structures based on their shapes and threedimensional conformations. Root mean square deviation (RMSD), a frequently-used approach, measures the average distance between the selected atoms of superimposed proteins. Although the RMSD is most popularly implemented, it suffers from a few drawbac...

Study of PKA binding sites in cAMP-signaling pathway using structural protein-protein interaction networks

Backgroud: Protein-protein interaction, plays a key role in signal transduction in signaling pathways. Different approaches are used for prediction of these interactions including experimental and computational approaches. In conventional node-edge protein-protein interaction networks, we can only see which proteins interact but ‘structural networks’ show us how these proteins inter...

Parallel Algorithm for Fast Cloth Simulation