Glucokinase (GK) is involved in normal glucose homeostasis and therefore it is a valid target for drug design and discovery efforts. GK activators (GKAs) have excellent potential as treatments of hyperglycemia and diabetes. The combined recent interest in GKAs, together with docking limitations and shortages of docking validation methods prompted us to use our new 3D-QSAR analysis, namely, dock...

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...

In this work we develop a method for fluid dynamically driven assembly in three dimensions and demonstrate its applicability to the development of programmable matter. Towards this end, we investigate docking of a single block onto a larger structure using detailed numerical simulations and experiments. Our simulation results show that a block whose degrees of freedom are limited is able to ali...

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 ...

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...

ATP is involved in numerous biochemical reactions in living cells interacting with different proteins. Molecular docking simulations provide considerable insight into the problem of molecular recognition of this substrate. To improve the selection of correct ATP poses among those generated by docking algorithms we propose a post-docking reranking criterion. The method is based on detailed analy...

The acquired immunodeficiency syndrome (AIDS) is a serious worldwide disease caused by the human immunodeficiency virus (HIV) infection. Recent research has pointed out that the G protein-coupled chemokine receptor CXCR4 and the coreceptor C-C chemokine receptor type 5 (CCR5) are important targets for HIV infection. The traditional Chinese medicine (TCM) database has been screened for candidate...

Docking simulates molecular interactions. Protein protein docking, owing to the sizes of molecules, is a very challenging problem. As the number of degrees of freedom in the molecular structure of proteins is huge, docking algorithms consider the molecules as relatively rigid bodies. Shape matching of two protein molecules is computationally difficult because the possibilities of matching the m...

The interaction between [Pt(phen)(pyrr-dtc)]NO3 (where phen = 1,10-phenanthroline and pyrr-dtc =pyrrolidinedithiocarbamat) with human serum albumin (HSA) was studied by fluorescence, UV–vis absorption, circular dichroism (CD) spectroscopy and molecular docking technique under like physiological condition in Tris–HCl buffer solution at pH 7.4. UV-Vis absorption spectroscopy indicates that the pro...