The docking field has come of age. The time is ripe to present the principles of docking, reviewing the current state of the field. Two reasons are largely responsible for the maturity of the computational docking area. First, the early optimism that the very presence of the "correct" native conformation within the list of predicted docked conformations signals a near solution to the docking pr...

Molecular docking is an efficient method to predict the conformations adopted by the ligand within the target binding site. Usually, standard docking protocol involves only one structure to represent the receptor, overlooking the changes in the binding pocket geometry induced by ligand binding. In our previous work, we observed that different conformations of the same target show different volu...

UNLABELLED The aim of this study is to determine the affinity of six active compounds of Aegle Marmelos Correa, they are (E, R)-Marmin, skimmianine, (S)-aegeline, aurapten, zeorin, and dustanin as antihistamines in histamine H1 receptor in comparison to cetirizin, diphenhydramine and chlorpheniramine as ligands comparison. Previously, in the in vitro study marmin obviously antagonized the hista...

Pistagremic acid (PA) is a bioactive triterpenoid isolated from various parts of Pistacia integerrima plants. The aim of this research was to investigate PA for reversion of multidrug resistant (MDR) mediated by P-glycoprotein using rhodamine-123 exclusion study on a multidrug resistant human ABCB1 (ATP-binding cassette, sub-family B, member 1) gene-transfected mouse T-lymphoma cell line in vit...

Synaptic vesicles dock to the plasma membrane at synapses to facilitate rapid exocytosis. Docking was originally proposed to require the soluble N-ethylmaleimide-sensitive fusion attachment protein receptor (SNARE) proteins; however, perturbation studies suggested that docking was independent of the SNARE proteins. We now find that the SNARE protein syntaxin is required for docking of all vesic...

This study aimed to predict the binding affinity, orientation, and physical interaction between limonene fat mass obesity-associated protein. The mechanism of protein association was explored by molecular docking, a bioinformatic tool. results were compared with reported anti-obesity drug such as orlistat flavonoids. AutoDock Vina tools used for docking PyMol Discovery Studio Visualizer visuali...

Evolutionary approaches to molecular docking typically use a realvalue encoding with standard genetic operators. Mutation is usually based on Gaussian and Cauchy distributions whereas for crossover no special considerations are made. The choice of operators is important for an efficient algorithm for this problem. We investigate their effect by performing a locality, heritability and heuristic ...

Cross-docking is a distribution strategy that enables the consolidation of less-thantruckload shipments into full truckloads without long-term storage. Due to the absence of a storage buffer inside a cross-dock, local and network-wide cross-docking operations need to be carefully synchronized. This paper proposes a framework specifying the interdependencies between different cross-docking probl...

Background: The present study was conducted to investigate the antinociceptive activity of methanol extract of Macaranga denticulata (Met.MD) in an animal model, followed by molecular docking analysis. Methods: Antinociceptive activity was determined by acetic acid-induced writhing and formalin-induced licking test in mice. Then, molecular docking study was performed to identify compounds havin...