We describe the testing and release of AutoDock4 and the accompanying graphical user interface AutoDockTools. AutoDock4 incorporates limited flexibility in the receptor. Several tests are reported here, including a redocking experiment with 188 diverse ligand-protein complexes and a cross-docking experiment using flexible sidechains in 87 HIV protease complexes. We also report its utility in an...

Keywords: DHFR-inhibiting activity, pteridine, furo[3,2-g]pteridine, molecular docking, QSAR-analysis

In this paper, we introduce a system named Comparative Molecular Interaction Profile Analysis system (CoMIPA) that utilizes virtual docking study for comprehensive analysis of molecular interactions. Research of RNA aptamer is very useful to creation of functional molecules, because RNA aptamer is excellent in binding selectivity and the stability of structure. By using 3-bases RNA fragment, th...

With the help of pharmacophore analysis and docking investigation, 15 novel 1-(4,4,5,5-tetramethyl-2-(3-nitrophenyl)-4,5-dihydroimidazol-1-yl)-oxyacetyl-L-amino acids (6a-o) were designed, synthesized, and assayed. On tail-flick and xylene-induced ear edema models, 10 μmol/kg 6a-o exhibited excellent oral anti-inflammation and analgesic activity. The dose-dependent assay of their representative...

cross docking is a logistic strategy that plays the role of a middle knot in distribution network in the provision process. in logistic part, inventory holding is considered as an important matter in managing costs. not only cross docking reduces the inventory holding cost, but it also reduces the cost of collecting received orders, transportation and duration of sending. the products, which ar...

Molecular field topology analysis, scaffold hopping, and molecular docking were used as complementary computational tools for the design of repellents for Aedes aegypti, the insect vector for yellow fever, chikungunya, and dengue fever. A large number of analogues were evaluated by virtual screening with Glide molecular docking software. This produced several dozen hits that were either synthes...

From in silico docking and COMPARE analysis, novel inhibitors of human NAD(P)H quinone oxidoreductase (NQO1) have been identified from the NCI compound database, the most potent of which has an observed IC(50) of 0.7muM. The inhibitors exhibit a diverse range of scaffolds. The ability of docking calculations to predict experimentally determined binding affinities for NQO1 is discussed, consider...

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...