Interactive haptics-assisted docking provides a virtual environment for the study of molecular complex formation. It enables the user to interact with the virtual molecules, experience the interaction forces via their sense of touch, and gain insights about the docking process itself. Here we use a recently developed haptics software tool, Haptimol_RD, for the rigid docking of protein subunits ...

Abstract: Aim and Background: Mycobacterium tuberculosis (TB) remains the leading cause of human death posing one most serious threats to public health around world. New strategies need be developed combat growing danger by multidrug resistance. The present study aims screen three different compounds inhibiting binding pocket Regulatory Repressor Protein EthR tuberculosis. In this we performed ...

Molecular docking simulations of fully flexible protein receptor (FFR) models are coming of age. In our studies, an FFR model is represented by a series of different conformations derived from a molecular dynamic simulation trajectory of the receptor. For each conformation in the FFR model, a docking simulation is executed and analyzed. An important challenge is to perform virtual screening of ...

Training machine learning algorithms with protein-ligand descriptors has recently gained considerable attention to predict binding constants from atomic coordinates. Starting from a series of recent reports stating the advantages of this approach over empirical scoring functions, we could indeed reproduce the claimed superiority of Random Forest and Support Vector Machine-based scoring function...

BACKGROUND: Despite the available range of lipid-lowering drugs, mainly synthetic origin, problem atherosclerosis therapy and its manifestations remain unresolved. Bioinformatics methods, in particular molecular docking, are considered as a promising direction terms developing effective original drugs. Today, source natural agents, it is advisable to consider terpenoids, namely sesquiterpene la...

In this work, we present a synchronous co-simulation of 6DOF (six degree freedom) ball and plate platform its 3D computer model. The in the virtual environment is intended to mimic rendezvous between cargo vehicle such as Falcon 9 from SpaceX ISS (International Space Station). visual feedback sensing position implemented using Kinect RGB-D device. human loop acts supervisory control for initiat...

AutoDock Vina, a new program for molecular docking and virtual screening, is presented. AutoDock Vina achieves an approximately two orders of magnitude speed-up compared with the molecular docking software previously developed in our lab (AutoDock 4), while also significantly improving the accuracy of the binding mode predictions, judging by our tests on the training set used in AutoDock 4 deve...

In this paper, we introduce a system named Comparative Molecular Interaction Profile Analysis system (CoMIPA) that utilizes virtual docking study for comprehensive analysis of molecular interactions. Research of RNA aptamer is very useful to creation of functional molecules, because RNA aptamer is excellent in binding selectivity and the stability of structure. By using 3-bases RNA fragment, th...