The necessity of treating receptor flexibility in proteinligand docking has been widely acknowledged and is the subject of extensive research in the field of drug discovery [1]. The use of multiple discrete protein conformations, so-called ensemble docking, has been proven to be a valid concept to mimic target plasticity in docking experiments [2,3]. Using molecular dynamics (MD) the number of ...

p53, as a transcription factor, plays an eminent role in tumor suppression. Y220C, a substitution mutation, which cause major structural changes in the protein, is evidenced to form a new protein cavity. This cavity is reckoned to accommodate small drug candidates, which may play a key role in cancer suppression. In the present, study we have tried to determine a drug candidate based on structu...

Flaviviral protease inhibitors identied by fragment-based library docking into a structure generated by molecular dynamics

The anti-obesity potential of various plant extracts and their associated bioactive compounds is well known. Molecular docking studies FTO with flavonoids, using Orlistat (an drug) as a control, were performed to identify the effects Rhamnus’ flavonoids (Obesity obesity protein). Prior molecular simulation, Rhamnus flavanoids analysed AutoDockTools (version 1.5.6). Docking simulations interacti...

The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking hepa...

This paper presents a new method for a six degrees of freedom haptic feedback in molecular docking simulations in virtual reality. The proposed method allows haptic interaction even in the case of classical molecular simulation which implies notoriously long computation time. These simulations are based on the Newtonian mechanics theory and imply an energetic interaction description between ato...

The prostanoid receptor EP1 is a G-protein-coupled receptor (GPCR) known to be involved in a variety of pathological disorders such as pain, fever and inflammation. These receptors are important drug targets, but design of subtype specific agonists and antagonists has been partially hampered by the absence of three-dimensional structures for these receptors. To understand the molecular interact...

The Hardware-In-the-Loop (HIL) simulation system for on-orbit docking dynamics is a large-scale complex test equipment. It establishes working conditions for the docking mechanism similar with those on orbit. The kernel of above dynamics HIL simulation system is a mechanical force and movement actions simulator. Besides the mechanical force and movement actions simulator, it also includes an en...