Toward structure prediction of cyclic peptides

H Yu, YS Lin - Physical Chemistry Chemical Physics, 2015 - pubs.rsc.org
Physical Chemistry Chemical Physics, 2015pubs.rsc.org
Cyclic peptides are a promising class of molecules that can be used to target specific protein–
protein interactions. A computational method to accurately predict their structures would
substantially advance the development of cyclic peptides as modulators of protein–protein
interactions. Here, we develop a computational method that integrates bias-exchange
metadynamics simulations, a Boltzmann reweighting scheme, dihedral principal component
analysis and a modified density peak-based cluster analysis to provide a converged …
Cyclic peptides are a promising class of molecules that can be used to target specific protein–protein interactions. A computational method to accurately predict their structures would substantially advance the development of cyclic peptides as modulators of protein–protein interactions. Here, we develop a computational method that integrates bias-exchange metadynamics simulations, a Boltzmann reweighting scheme, dihedral principal component analysis and a modified density peak-based cluster analysis to provide a converged structural description for cyclic peptides. Using this method, we evaluate the performance of a number of popular protein force fields on a model cyclic peptide. All the tested force fields seem to over-stabilize the α-helix and PPII/β regions in the Ramachandran plot, commonly populated by linear peptides and proteins. Our findings suggest that re-parameterization of a force field that well describes the full Ramachandran plot is necessary to accurately model cyclic peptides.
The Royal Society of Chemistry
以上显示的是最相近的搜索结果。 查看全部搜索结果