We have developed a new tool for virtual database screening. This tool, referred to as the Generic Evolutionary Method for molecular DOCKing (GEMDOCK), combines an evolutionary approach and a new pharmacophore-based scoring function. The former integrates discrete and continuous global search strategies with local search strategies to speed up convergence. The latter simultaneously serves as th...

SUMMARY Protein-protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict str...

Understanding energetics and mechanism of protein-protein association remains one of the biggest theoretical problems in structural biology. It is assumed that desolvation must play an essential role during the association process, and indeed protein-protein interfaces in obligate complexes have been found to be highly hydrophobic. However, the identification of protein interaction sites from s...

BACKGROUND This study examined the hypothesis that 26S proteasome dysfunction in human end-stage heart failure is associated with decreased docking of the 19S regulatory particle to the 20S proteasome. Previous studies have demonstrated that 26S proteasome activity is diminished in human end-stage heart failure associated with oxidation of the 19S regulatory particle Rpt5 subunit. Docking of th...

Motivation: An effective docking algorithm for antibody–protein antigen complex prediction is an important first step toward design of biologics and vaccines. We have recently developed a new class of knowledge-based interaction potentials called Decoys as the Reference State (DARS) and incorporated DARS into the docking program PIPER based on the fast Fourier transform correlation approach. Al...

The anti-ESBL activity of 1, 2-benzenedicarboxylic acid, mono (2-ethylhexyl) ester (DMEHE) extracted from marine Streptomyces sp strain VITSJK8 was further confirmed by in silico analysis. A total of 10 ESBL proteins was chosen for this study from the protein data bank (PDB) and were docked with the DMEHE. The resultant atomic contact energy (ACE) was compared with dockings of known antibiotic ...

Cells are interactive living systems where proteins movements, interactions and regulation are substantially free from centralized management. How protein physico-chemical and geometrical properties determine who interact with whom remains far from fully understood. We show that characterizing how a protein behaves with many potential interactors in a complete cross-docking study leads to a sha...

Protein-protein interactions play a key part in most biological processes and understanding their mechanism is a fundamental problem leading to numerous practical applications. The prediction of protein binding sites in particular is of paramount importance since proteins now represent a major class of therapeutic targets. Amongst others methods, docking simulations between two proteins known t...

because of participation in many aspects of human life, and due to oxidation-sensitive characteristics of dopamine (da) and arachidonoyl dopamine (aa-da), the necessity of biocompatible carrier to keep them against oxidation is of importance. in this work, we explored the putative binding sites of da and aa-da to -lactoglobulin (blg) as potent carrier. docking results identified the binding si...

curcumin (cur) is the active curcuminoid with many physiological, biochemical, and pharmacological properties. solubility and stability of cur is the limiting factors for realizing its therapeutic potential. bovine β-casein is an abundant milk protein that is highly amphiphilic and self-assembles into stable micellar nanoparticles in aqueous solution. β-casein nanoparticle can solubilize cur mo...