In order to improve docking score correction, we developed several structure-based quantitative structure activity relationship (QSAR) models by protein-drug docking simulations and applied these models to public affinity data. The prediction models used descriptor-based regression, and the compound descriptor was a set of docking scores against multiple (∼600) proteins including nontargets. Th...

In this study, a new molecular docking method is presented to improve the docking accuracy. We introduce to docking design a concept of residue groups based on induced-fit and use K Score (a kind of PMF scoring function) to score the docking position. Genetic algorithm with the multi-population evolution and entropy-based searching technique with narrowing down space is used to solve the optimi...

Physical interactions between proteins are involved in many important cell functions and are key for understanding the mechanisms of biological processes. Protein-protein docking programs provide a means to computationally construct three-dimensional (3D) models of a protein complex structure from its component protein units. A protein docking program takes two or more individual 3D protein str...

MOTIVATION The limited success rate of protein-protein docking procedures is generally attributed to structure differences between the bound and unbound states of the molecules. Herein we analyze a large dataset of protein-protein docking results and identify additional parameters that affect the performance of docking procedures. RESULTS We find that the distinction between nearly correct mo...

Based on the results of several groups using different docking methods, the key properties that determine the expected success rate in protein-protein docking calculations are measures of conformational change, interface area, and hydrophobicity. A classification of protein complexes in terms of these measures provides a prediction of docking difficulty. This classification is used to study the...

With the advancement of novel techniques in drug discovery, various approaches have been used in the structure based drug designing. One of the most important strategies is molecular docking. The study of molecular docking and simulation deals with the intermolecular interaction of drug targets i.e. proteins, nucleic acids, lipids and ligands. The aim of molecular docking is to achieve an optim...

Secretory vesicles dock at the plasma membrane before they undergo fusion. Molecular docking mechanisms are poorly defined but believed to be independent of SNARE proteins. Here, we challenged this hypothesis by acute deletion of the target SNARE, syntaxin, in vertebrate neurons and neuroendocrine cells. Deletion resulted in fusion arrest in both systems. No docking defects were observed in syn...

Prediction of the bound configuration of small-molecule ligands that differ substantially from the cognate ligand of a protein co-crystal structure is much more challenging than re-docking the cognate ligand. Success rates for cross-docking in the range of 20-30 % are common. We present an approach that uses structural information known prior to a particular cutoff-date to make predictions on l...

It is important to understand factors that may influence responses to stress, as these factors may also influence vulnerability to pathologies that can develop when stress responses are excessive or prolonged. It is clear that, in adults, the sex of an individual can influence the cortisol response to stress in a stressor specific manner. Nevertheless, the stage of development at which these se...

More and more researches on household mobile robots are being undertaken these days. Since commercial cleaning robots are now available for sale to the public, robots are being used in private homes. As the quality of household robots improves, docking stations, which have a variety of uses, including as automatic recharging ports, have become increasingly important. Generally in household robo...