Premium
New Trends in Inspecting GPCR‐ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova
Author(s) -
Ciancetta Antonella,
Cuzzolin Alberto,
Deganutti Giuseppe,
Sturlese Mattia,
Salmaso Veronica,
Cristiani Andrea,
Sabbadin Davide,
Moro Stefano
Publication year - 2016
Publication title -
molecular informatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.481
H-Index - 68
eISSN - 1868-1751
pISSN - 1868-1743
DOI - 10.1002/minf.201501011
Subject(s) - computer science , g protein coupled receptor , computational biology , docking (animal) , molecular dynamics , ligand (biochemistry) , molecular model , nanotechnology , chemistry , computational chemistry , biology , materials science , stereochemistry , receptor , medicine , biochemistry , nursing
In this review, we present a survey of the recent advances carried out by our research groups in the field of ligand‐GPCRs recognition process simulations recently implemented at the Molecular Modeling Section (MMS) of the University of Padova. We briefly describe a platform of tools we have tuned to aid the identification of novel GPCRs binders and the better understanding of their binding mechanisms, based on two extensively used computational techniques such as molecular docking and MD simulations. The developed methodologies encompass: (i) the selection of suitable protocols for docking studies, (ii) the exploration of the dynamical evolution of ligand‐protein interaction networks, (iii) the detailed investigation of the role of water molecules upon ligand binding, and (iv) a glance at the way the ligand might go through prior reaching the binding site.