Robust Conformational Space Exploration of Cyclic Peptides by Combining Different MD Protocols and Force Fields.

ABSTRACT: Cyclic peptides are an important class of pharmaceutical drugs. We used replica-exchange molecular dynamics (REMD) and simulated tempering (ST) simulations to explore the conformational landscape of a set of nine cyclic peptides. The N-ter to C-ter backbone-cyclized peptides of 7-10 residues were previously designed for high conformational stability with a mixture of l- and d-amino acids. Their experimental NMR structures are available in the protein data bank (PDB). For each peptide, we tested several force fields, namely, Amber96, Amber14, RSFF2C, and Charmm36m in implicit and explicit solvents. We find that the variability of the free energy maps obtained from several protocols is larger than the variability obtained by just repeating the same protocol. Running multiple protocols is the

SUBMITTER: Murail S 

PROVIDER: S-EPMC12661557 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature