title: New Trends in Inspecting GPCR-ligand Recognition Process: the Contribution of the Molecular Modeling Section (MMS) at the University of Padova.
abstract: 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.
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Ciancetta
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Cuzzolin
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Deganutti
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
authors.forename: Mattia
authors.initials: M
authors.lastname: Sturlese
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
authors.forename: Veronica
authors.initials: V
authors.lastname: Salmaso
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
authors.forename: Andrea
authors.initials: A
authors.lastname: Cristiani
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Sabbadin
authors.affiliation: Molecular Modeling Section (MMS), Department of Pharmaceutical and Pharmacological Sciences, University of Padova via Marzolo 5, Padova, Italy. stefano.moro@unipd.it.
authors.forename: Stefano
authors.initials: S
authors.lastname: Moro
mesh_terms: D001665:Binding Sites / Q000502:physiology; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D062105:Molecular Docking Simulation / Q000379:methods; D056004:Molecular Dynamics Simulation; D011485:Protein Binding / Q000502:physiology; D043562:Receptors, G-Protein-Coupled / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D008024:Ligands; D043562:Receptors, G-Protein-Coupled
keywords: Adenosine Receptors; DockBench; G-protein Coupled Receptors (GPCRs); Homology Modeling; Molecular Docking; Molecular Dynamics; Supervised Molecular Dynamics