Atomevo: a web server combining protein modelling, docking, molecular dynamic simulation and MMPBSA analysis of Candida antarctica lipase B (CalB) fusion protein.

Although current computational biology software is available and has prompted the development of enzyme-substrates simulation, they are difficult to install and inconvenient to use. This makes the time-consuming and error-prone process. By far there is still a lack of a complete tool which can provide a one-stop service for the enzyme-substrates simulation process.

Molecular Dynamic Simulation of the Porcine Pancreatic Lipase in Non-aqueous Organic Solvents.

This paper investigates the conformational stability of porcine pancreatic lipase (PPL) in three non-aqueous organic solvents, including dimethyl sulfoxide (DMSO), propylene glycol (PRG), and ethanol (EtOH) through molecular dynamic (MD) simulation. The root mean square deviations (RMSDs), radius of gyration (Rg), solution accessible surface area (SASA), radial distribution function (RDF), hydrogen bond (H-bond), Ramachandran plot analysis, secondary structure, and enzyme substrate affinity of the PPL in the various organic solvents were comparatively investigated. The results showed that the backbone and active pocket RMSD, and hydrophilic ASA of PPL in three solvents increase with the increase in the solvent LogP, while the Rg, hydrophobic ASA, and H-bond between the solvent and PPL decrease.