We have developed a computational pipeline for the prediction of protein-small molecule interactions and have applied it to the drug repositioning problem through a large-scale analysis of known drug targets and small molecule drugs. Our pipeline combines forward and inverse docking, the latter of which is a twist on the conventional docking procedure used in drug discovery: instead of docking ...

The urgent need for novel HIV-1-RT inhibitors with broad spectrum chemotherapeutic properties has provided an impetus for understanding the structural requisites of HIV-1-RT inhibitors at the molecular level. Toward this objective, binding mode analysis of 113 benzimidazole analogs was performed. First, molecular docking studies were performed on novel benzimidazoles by Glide program in the act...

  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 ...

It is well known that computer-aided docking of large ligands, with many rotatable bonds, is extremely difficult. AutoDock is a widely used docking program that can dock small ligands, with upto 5 or 6 rotatable bonds, accurately and quickly. Docking of larger ligands, however, is not very accurate and is computationally expensive. In this paper we present an AutoDock-based incremental docking ...

The results from reiterated docking experiments may be used to evaluate an empirical vibrational entropy of binding in ligand-protein complexes. We have tested several methods for evaluating the vibrational contribution to binding of 22 nucleotide analogues to the enzyme APS reductase. These include two cluster size methods that measure the probability of finding a particular conformation, a me...

This article gives an overview of recent progress in protein-protein docking and it identifies several directions for future research. Recent results from the CAPRI blind docking experiments show that docking algorithms are steadily improving in both reliability and accuracy. Current docking algorithms employ a range of efficient search and scoring strategies, including e.g. fast Fourier transf...

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...

UNLABELLED A method is described for the analysis of the results obtained from the docking studies applied on a protein target and small molecules chemical compounds as ligands from various sources using different docking tools. We show the use of Dempster Shafer Theory (DST) to select the high ranking top compounds for further analysis and consideration. AVAILABILITY Application is freely av...

Based on a protein-protein docking approach we have developed a procedure to verify or falsify protein-protein interactions that were proposed by other methods such as yeast-2-hybrid assays. Our method currently utilizes intermolecular energies but can be expanded to incorporate additional terms such as amino acid based pair-potentials. We show some early results that demonstrate the general ap...

Obesity refers to abnormal or excessive fat accumulation in the human body which results in health risk. Obesity leads to several risk factors for a number of chronic diseases such as diabetes, cardiovascular diseases, cancer and osteoarthritis. Curcumin, the major polyphenol of turmeric spice, is a member of the ginger family (Zingiberaceae). Growth of adipose tissue is enhanced by the process...