Little information is available regarding a circulating HIV genotype among high-risk groups in Afghanistan; we describe HIV genotypes among injecting drug users (IDUs) and sex workers (SWs) in four Afghan cities. Participants completed behavioral questionnaires and HIV testing. Western blot-confirmed specimens had peripheral mononuclear blood cells isolated for genotyping. Analysis of recombina...

GST family genes have a critical role in xenobiotic metabolism and drug resistance. Among the GST family the GST-μ, GST-π, GST-α and GST-θ are the most abundant classes and have a major role in the carcinogen detoxification process. Nevertheless the activity of these enzymes may differ due to polymorphisms which ultimately results in interindividual susceptibility to cancer development. In this...

Molecular docking is an important component of computer-aided drug discovery. In this communication, we describe GeauxDock, a new docking approach that builds on the ideas of ligand homology modeling. GeauxDock features a descriptor-based scoring function integrating evolutionary constraints with physics-based energy terms, a mixed-resolution molecular representation of protein-ligand complexes...

Cytochrome P450 BM3 (P450 102) from Bacillus megaterium is a unique bacterial P450, formed from the fusion of a fatty acid hydroxylase to a eukaryotic-like NADPH-cytochrome P450 reductase flavoprotein in a single (1 19 kDa) polypeptide chain (1, 2). It is an attractive model system for enzymological and structural studies due to its homology with mammalian drug metabolising P450 systems, and wi...

The fusion protein of respiratory syncytial virus (RSV-F) is responsible for fusion of virion with host cells and infection of neighbouring cells through the formation of syncytia. A three-dimensional model structure of RSV-F was derived by homology modelling from the structure of the equivalent protein in Newcastle disease virus (NDV). Despite very low sequence homology between the two structu...

Motivation The high cost of drug discovery motivates the development of accurate virtual screening tools. Binding-homology, which takes advantage of known protein-ligand binding pairs, has emerged as a powerful discrimination technique. In order to exploit all available binding data, modelled structures of ligand-binding sequences may be used to create an expanded structural binding template li...

Conjugative transposition drives the emergence of multidrug resistance in diverse bacterial pathogens, yet the mechanisms are poorly characterized. The Tn1549 conjugative transposon propagates resistance to the antibiotic vancomycin used for severe drug-resistant infections. Here, we present four high-resolution structures of the conserved Y-transposase of Tn1549 complexed with circular transpo...

Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, gene expression, etc. Accurate prediction of protein-ligand binding affinities is vital to rational drug design and the understanding of protein-ligand binding and binding induced function. Existing...

We introduce several geometric notions, including the width of a homology class, to theory persistent homology. These ideas provide interpretations persistence diagrams. Indeed, we give quantitative and descriptions “life span” or “persistence” class. As case study, analyze power filtration on unweighted graphs explicit bounds for life spans classes in diagrams all dimensions.

This study was performed to find the selective chemical features for Aurora kinase-B inhibitors using the potent methods like Hip-Hop, virtual screening, homology modeling, molecular dynamics and docking. The best hypothesis, Hypo1 was validated toward a wide range of test set containing the selective inhibitors of Aurora kinase-B. Homology modeling and molecular dynamics studies were carried o...