Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) worldwide has increased the importance of computational tools to design a drug or vaccine in reduced time with minimum risk. Earlier studies have emphasized important role RNA-dependent RNA polymerase (RdRp) SARS-CoV-2 replication as potential target. In our study, comprehensive approaches were applied identify compounds targeting RdR...

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, ...

Abstract: This paper investigates the optimal rendezvous with power-limited propulsion systems and collision avoidance. A 26-state dynamic model is established including both translational and rotational dynamics. This model is effective for describing autonomous rendezvous with both a three-axis attitude stabilized target and a tumbling one. Collisions are prevented through setting a safety sp...

A novel approach to incorporate water molecules in protein-ligand docking is proposed. In this method, the water molecules display the same flexibility during the docking simulation as the ligand. The method solvates the ligand with the maximum number of water molecules, and these are then retained or displaced depending on energy contributions during the docking simulation. Instead of being a ...

UNLABELLED Structural analysis of the high-mobility group protein B1 (HMGB1)-DNA complex and a docking simulation between glycyrrhetinic acid (GA) and the HMGB1-DNA complex were performed with a software package the Molecular Operating Environment (MOE). An HMGB1-DNA (PDB code: 2GZK) was selected for the 3D structure modeling of the HMGB1-DNA complex. The Site Finder module of the MOE identifie...

Histone tails play an important role in nucleosome structure and dynamics. Here we investigate the effect of truncation of histone tails H3, H4, H2A and H2B on nucleosome structure with 100 ns all-atom molecular dynamics simulations. Tail domains of H3 and H2B show propensity of α-helics formation during the intact nucleosome simulation. On truncation of H4 or H2B tails no structural change occ...

Bioflavonoids are the largest group of plant-derived polyphenolic compounds with diverse biological potential and have also been proven efficacious in treatment Severe Acute Respiratory Syndrome (SARS) Middle East (MERS). The present investigation validates molecular docking, simulation, MM-PBSA studies fifteen bioactive bioflavonoids derived from plants as a plausible antiviral COVID-19. Molec...

Background: Cyclic adenosine monophosphate (cAMP) dependent protein kinase A plays major role in cell signalling to undergo many cellular functions. Over expression of extracellular cAMP dependent protein kinase catalytic subunit alpha (PRKACA) causes severe tumorgenesis in prostate. Thus, computer aided high throughput virtual screening and molecular dynamics simulations studies were implement...

Undecaprenyl pyrophosphate synthase is a cis-prenyltransferase enzyme, which is required for cell wall biosynthesis in bacteria. Undecaprenyl pyrophosphate synthase is an attractive target for antimicrobial therapy. We performed long molecular dynamics simulations and docking studies on undecaprenyl pyrophosphate synthase to investigate its dynamic behavior and the influence of protein flexibil...