SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations - Université de Lille
Article Dans Une Revue Journal of Chemical Information and Modeling Année : 2022

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

Résumé

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 opensource 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.
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Dates et versions

hal-04077236 , version 1 (21-04-2023)

Identifiants

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Corentin Bedart, Nicolas Renault, Philippe Chavatte, Adeline Porcherie, Abderrahim Lachgar, et al.. SINAPs: A Software Tool for Analysis and Visualization of Interaction Networks of Molecular Dynamics Simulations. Journal of Chemical Information and Modeling, 2022, 62 (6), pp.1425-1436. ⟨10.1021/acs.jcim.1c00854⟩. ⟨hal-04077236⟩
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