Updating RoNBio molecular modelling system to support in silico investigation of AMP activity on membrane models

摘要

The RoNBio molecular modelling system was initially developed to study Gram-negative membrane, and was recently updated to support the investigation of antimicrobial peptides (AMP) activity on lipid bilayers. The system consists of an extensible and scalable pool of HTC and HPC resources which are accessible to the user through a graphical frontend. Data handling and processing is accomplished by various retrieval, conversion and modelling tools, and is managed by means of automatic, programmable and reusable Taverna workflows. The global concern regarding the rapid emergence of multidrug-resistant pathogens in the last decade has prompted the search for alternative treatments like repurposing approved drugs or AMPs. AMPs that are produced by bacteria, insects, or chemically synthetized are very promising due to their natural antimicrobial proprieties and low propensity for development of resistance by microorganisms. The recently added workflows to RoNBio employs various tools that automates the analysis of molecular dynamics simulations meant to investigate the in silico activity of AMPs on lipid bilayers, including: membrane thickness, area per lipid (APL), AMP distribution across the bilayer surface, and AMP binding energy with the membrane using APBS.