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Hybrid MM/CG Webserver: Automatic Set Up of Molecular Mechanics/Coarse-Grained Simulations for Human G Protein-Coupled Receptor/Ligand Complexes

Jakob Schneider, Rui Ribeiro, Mercedes Alfonso-Prieto, Paolo Carloni, Alejandro Giorgetti
2020 Frontiers in Molecular Biosciences  
Hybrid Molecular Mechanics/Coarse-Grained (MM/CG) simulations help predict ligand poses in human G protein-coupled receptors (hGPCRs), the most important protein superfamily for pharmacological applications  ...  This approach allows the description of the ligand, the binding cavity, and the surrounding water molecules at atomistic resolution, while coarse-graining the rest of the receptor.  ...  ACKNOWLEDGMENTS We thank Emiliano Ippoliti for the setup of the server and Jonas Goßen for programming advice.  ... 
doi:10.3389/fmolb.2020.576689 pmid:33102525 pmcid:PMC7500467 fatcat:6fwfr6nunvb5fo2tgnvnrq4axm

Predicting ligand binding poses for low-resolution membrane protein models: Perspectives from multiscale simulations

Jakob Schneider, Ksenia Korshunova, Francesco Musiani, Mercedes Alfonso-Prieto, Alejandro Giorgetti, Paolo Carloni
2018 Biochemical and Biophysical Research Communications - BBRC  
low-resolution homology models are available. • Our molecular mechanics/coarse grained approach improves ligand pose predictions.  ...  It is especially tailored for G-protein coupled receptors, the largest membrane receptor family in humans.  ...  We also acknowledge the financial support of the "Ernesto Illy Foundation" (Trieste, Italy), as well as grants (to P.C.) from the  ... 
doi:10.1016/j.bbrc.2018.01.160 pmid:29409902 fatcat:wxl25mf5yrafbcu4pjuouqh4ey

From System Modeling to System Analysis: The Impact of Resolution Level and Resolution Distribution in the Computer-Aided Investigation of Biomolecules

Marco Giulini, Marta Rigoli, Giovanni Mattiotti, Roberto Menichetti, Thomas Tarenzi, Raffaele Fiorentini, Raffaello Potestio
2021 Frontiers in Molecular Biosciences  
The ever increasing computer power, together with the improved accuracy of atomistic force fields, enables researchers to investigate biological systems at the molecular level with remarkable detail.  ...  In particular, we discuss two distinct yet complementary aspects of protein modeling: on the one hand, the relationship between the resolution of a model and its capacity of accurately reproducing the  ...  G. (2014). Predictive Energy Landscapes (2012). Hybrid Molecular Mechanics/coarse-Grained Simulations for for Folding -helical Transmembrane Proteins. Proc. Natl. Acad.  ... 
doi:10.3389/fmolb.2021.676976 pmid:34164432 pmcid:PMC8215203 fatcat:cdq7tvurlnbyfp6lv4kainczhm