TY  - JOUR
SP  - 205
UR  - https://doi.org/10.1021/acs.jcim.3c01574
TI  - Extended Metadynamics Protocol for Binding/Unbinding Free Energies of Peptide Ligands to Class A G-Protein-Coupled Receptors
ID  - discovery10185650
SN  - 1549-9596
N1  - This version is the author accepted manuscript. For information on re-use, please refer to the publisher?s terms and conditions.
EP  - 218
JF  - Journal of Chemical Information and Modeling
AV  - public
N2  - A metadynamics protocol is presented to characterize the binding and unbinding of peptide ligands to class A G-protein-coupled receptors (GPCRs). The protocol expands on the one previously presented for binding and unbinding small-molecule ligands to class A GPCRs and accounts for the more demanding nature of the peptide binding-unbinding process. It applies to almost all class A GPCRs. Exemplary simulations are described for subtypes Y1R, Y2R, and Y4R of the neuropeptide Y receptor family, vasopressin binding to the vasopressin V2 receptor (V2R), and oxytocin binding to the oxytocin receptor (OTR). Binding free energies and the positions of alternative binding sites are presented and, where possible, compared with the experiment.
VL  - 64
IS  - 1
A1  - Calderón, Jacqueline C
A1  - Plut, Eva
A1  - Keller, Max
A1  - Cabrele, Chiara
A1  - Reiser, Oliver
A1  - Gervasio, Francesco L
A1  - Clark, Timothy
Y1  - 2024/01/08/
PB  - American Chemical Society
ER  -