Molecular docking computationally screens thousands to millions of organic molecules against protein structures, looking for those with complementary fits. Many approximations are made, often resulting in low "hit rates." A strategy to overcome these approximations is to rescore top-ranked docked molecules using a better but slower method. One such is afforded by molecular mechanics-generalized...

In recent years, an epidemic of the highly pathogenic avian influenza H7N9 virus has persisted in China, with a high mortality rate. To develop novel anti-influenza therapies, we have constructed a machine-learning-based scoring function (RF-NA-Score) for the effective virtual screening of lead compounds targeting the viral neuraminidase (NA) protein. RF-NA-Score is more accurate than RF-Score,...

in the present study, the antimicrobial tests of patchouli oil were studied by using molecular docking technology and antimicrobial test in vitro. five biological macromolecule enzymes, required by the bacteria in the process of biosynthesis were selected as target molecules. five antibiotics benzylpenicillin, sulfadiazine, trimethoprim, rifampicin and ciprofloxacin, which are generally acknowle...

the antidiuretic effect of arginine vasopressin (avp) is mediated by the vasopressin v2 receptor. the docking study of avp as a ligand to v2 receptor helps in identifying important amino acid residues that might be involved in avp binding for predicting the lowest free energy state of the protein complex. whereas previous researchers were not able to detect the exact site of the ligand-receptor...

objective(s): recently we reported that the soybean 15-lipoxygenase (slo) inhibitory activity of pyrimido[4,5-b][l,4]benzothiazines largely depends on the orientation of sulfur atom of thiazine core towards feiii-oh in the active site pocket of the enzyme with subsequent oxidation of sulfur to sulfoxide. in this paper the results of a comparative study on the slo inhibitory activities of the me...

background: luxi is a component of the quorum sensing signaling pathway in vibrio fischeri responsible for the inducer synthesis that is essential for bioluminescence. methods: homology modeling of luxi was carried out using phyre2 and refined with the galaxyweb server. five models were generated and evaluated by errat, anolea, qmean6, and procheck. results: five refined models were generated b...

Cross docking is a logistics strategy that strives to reduce inventory holding costs, shipping costs, and delays in delivering the products. In this research, an optimization model is presented for split loading and unloading products by suppliers and customers, vehicle routing with fuzzy possibilistic time window constraints among them, assignment of vehicles to cross dock, consolidation and i...

Protein receptor conformations, obtained from molecular dynamics (MD) simulations, have become a promising treatment of its explicit flexibility in molecular docking experiments applied to drug discovery and development. However, incorporating the entire ensemble of MD conformations in docking experiments to screen large candidate compound libraries is currently an unfeasible task. Clustering a...

Molecular docking is a complex optimization problem aimed at predicting the position of a ligand molecule in the active site of a receptor with the lowest binding energy. This problem can be formulated as a bi-objective optimization problem by minimizing the binding energy and the Root Mean Square Deviation (RMSD) difference in the coordinates of ligands. In this context, the SMPSO multi-object...