SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations

As long as the structural
study of molecular mechanisms requires
multiple molecular dynamics reflecting contrasted bioactive states,
the subsequent analysis of molecular interaction networks remains
a bottleneck to be fairly treated and requires a user-friendly 3D
view of key interactions. Structural Interaction Network Analysis
Protocols (SINAPs) is a proprietary python tool developed to (i) quickly
solve key interactions able to distinguish two protein states, either
from two sets of molecular dynamics simulations or from two crystallographic
structures, and (ii) render a user-friendly 3D view of these key interactions
through a plugin of UCSF Chimera, one of the most popular open-source
viewing software for biomolecular systems. Through two case studies,
glucose transporter-1 (GLUT-1) and A2A adenosine receptor (A2AR),
SINAPs easily pinpointed key interactions observed experimentally
and relevant for their bioactivities. This very effective tool was
thus applied to identify the amino acids involved in the molecular
enzymatic mechanisms ruling the activation of an immunomodulator drug
candidate, P28 glutathione-S-transferase (P28GST). SINAPs is freely
available at https://github.com/ParImmune/SINAPs.