Biomolecular Reaction and Interaction Dynamics Global Environment (BRIDGE) is an open-source
web platform developed with the aim to provide an environment for the design of …

This paper is a tutorial developed for the data analysis platform Galaxy. The purpose of Galaxy
is to make high-throughput computational data analysis, such as molecular dynamics, a …

ProtoCaller is a Python library distributed through Anaconda which automates relative
protein–ligand binding free energy calculations in GROMACS. It links a number of popular …

This study explores the potential application of rice bran (agro waste) to nano-encapsulate
phytase, which is a thermally unstable biologically active enzyme. Rice bran was converted to …

Motivation The pathway from genomics through proteomics and onto a molecular description
of biochemical processes makes the discovery of drugs and biomaterials possible. A …

Conspectus Enzyme reactions are complex to simulate accurately, and none more so than
glycoenzymes (glycosyltransferase and glycosidases). A rigorous sampling of the protein …

Protein-ligand binding prediction is central to the drug-discovery process. This often follows
an analysis of genomics data for protein targets and then protein structure discovery. …

When faced with the investigation of the preferential binding of a series of ligands against a
known target, the solution is not always evident from single structure analysis. An ensemble …

Animal trials and in vitro drug screening can improve drug discovery. However, such pre-
clinical screenings are often costly and time-consuming. Due to this, a more effective …

Objectives: Learn about force-fields and MD parameterization Learn how to conduct MD
simulation and analysis for a protein-ligand system Understand how different molecular …