Introduction: Interferon beta is one of the members of type I interferons. Creating R27T and V101F mutations is one of the important researches performed to improve function, decrease immunogenicity, increase expression and increase half-life of interferon beta. In this study, the effects of R27T and V101F mutations on interferon beta binding to interferon receptors were studied by molecular do...

Introduction: Interferon beta is one of the members of type I interferons. Creating R27T and V101F mutations is one of the important researches performed to improve function, decrease immunogenicity, increase expression and increase half-life of interferon beta. In this study, the effects of R27T and V101F mutations on interferon beta binding to interferon receptors were studied by molecular do...

Our previous study showed that a triterpene mixture, consisting of echinocystic acid (EA) and oleanolic acid (OA) at a ratio of 4 : 1, dose-dependently ameliorated the hyperlipidemia and atherosclerosis in rabbits fed with high fat/high cholesterol diets. This study was aimed at exploring the mechanisms underlying antihyperlipidemic effect of EA. Molecular docking simulation of EA was performed...

Objective: The purpose of this study was to determine the structural-based molecular interactions between flavonoids contained in Acalypha indica L. and caspase-3 by docking dynamics (MD) simulations.
 Methods: In a computer simulation, ten A. were evaluated for using X-ray crystal structure human (PDB ID 1NME). AutoDock 4.2 software used docking, MD simulations done with GROMACS v2018.&#x...

monoamine oxidase (ec, 1.4.3.4) or amine oxidoreductase catalyzes the oxidative deamination of biogenic amines. abnormal action of the monoamine oxidase b has been associated with neurological dysfunctions including parkinson´s disorder. monoamine oxidase b inhibitors divulged that these agents were effective in the therapeutic management of parkinson's disease. understanding the interaction of...

We present systemsDock, a web server for network pharmacology-based prediction and analysis, which permits docking simulation and molecular pathway map for comprehensive characterization of ligand selectivity and interpretation of ligand action on a complex molecular network. It incorporates an elaborately designed scoring function for molecular docking to assess protein-ligand binding potentia...

While FPGAs have only one fifth the raw floating point capability of GPUs, other attributes allow them to be surprisingly competitive with respect to a number of critical floating point intensive applications. In the first part we review these FPGA attributes. The bulk of this extended abstract then provides an overview of efficient FPGA implementations of Molecular Dynamics, Molecular Docking,...

The accurate prediction of a ligand-protein complex structure is important for computer-assisted drug development. Although many docking methods have been developed over the last three decades, the success of binding structure prediction remains greatly limited. The purpose of this study was to demonstrate the usefulness of molecular dynamics (MD) simulation in assessing a docking pose predicte...

Molecular docking is an important tool for the discovery of new biologically active molecules given that the receptor structure is known. An excellent environment for the development of new methods and improvement of the current methods is being provided by the rapid growth in the number of proteins with known structure. The evaluation of the solvation energies outstands among the challenges fo...

Virtual high-throughput screening (vHTS) is an invaluable method in modern drug discovery. It permits screening large datasets or databases of chemical structures for those structures binding possibly to a drug target. Virtual screening is typically performed by docking code, which often runs sequentially. Processing of huge vHTS datasets can be parallelized by chunking the data because individ...