MOTIVATION Water molecules are key players for protein folding and function. On the protein surface, water is not placed randomly, but display instead a particular structure evidenced by the presence of specific water sites (WS). These WS can be derived and characterized using explicit water Molecular Dynamics simulations, providing useful information for ligand binding prediction and design. H...

In silico methods are useful for predicting 3D structure of binding sites when experimental information is lack. The complex interaction between γ-crystallins and small ligands is a key element in understanding the lens transparency. In spite of the high sequence similarity of γ-crystallins, different numbers of pockets were automatically identified on their molecular surfaces. γC-crystallin ha...

Diabetes mellitus is one of the major disease currently affecting an estimated 143 million people worldwide and the number is growing rapidly. Now a day, as there is a renewed interest in the traditionally used herbal drugs, the present study was aimed to screen the identified constituents of Helicteres isora for determining the potent constituent with antidiabetic activity using insilico appro...

Conventional toxicology protocols and methods are resource-intensive. Hence, the integration of in silico methodologies with reproducible biological protocols is necessary to expedite the process. The present study focuses on the interaction of the homology modelled human Aryl hydrocarbon Receptor (hAHR) with 13 environmentally persistent organic pollutants that are implicated in endometriosis....

Molecular docking modelling was performed as previously described (Torrent et al., 2011). Briefl y, the docking simulations were performed using Autodock 4.2 (The Scripps Research Institute, La Jolla, CA, USA). The protein coordinates of the eight human RNases were taken from X-ray crystallography or NMR data. When no three-dimensional structure was available, the protein structures were predic...

In this work, we propose a deep learning approach to improve docking-based virtual screening. The deep neural network that is introduced, DeepVS, uses the output of a docking program and learns how to extract relevant features from basic data such as atom and residues types obtained from protein-ligand complexes. Our approach introduces the use of atom and amino acid embeddings and implements a...

Repurposing has gained momentum globally and become an alternative avenue for drug discovery because of its better success rate, and reduced cost, time and issues related to safety than the conventional drug discovery process. Several drugs have already been successfully repurposed for other clinical conditions including drug resistant tuberculosis (DR-TB). Though TB can be cured completely wit...