Docking Flexible Cyclic Peptides with AutoDock CrankPep.

Published in: Journal of chemical theory and computation (2019)

While a new therapeutic cyclic peptide is approved nearly every year, docking large macrocycles has remained challenging. Here, we present a new version of our peptide docking software AutoDock CrankPep (ADCP), extended to dock peptides cyclized through their backbone and/or side chain disulfide bonds. We show that within the top 10 solutions, ADCP identifies the proper interactions for 71% of a data set of 38 complexes, thus making it a useful tool for rational peptide-based drug design.

Keyphrases

molecular dynamics
molecular dynamics simulations
protein protein
genome wide
electronic health record
emergency department
gene expression
dna methylation
psychometric properties
artificial intelligence
drug administration