Ontology highlight
ABSTRACT:
SUBMITTER: Voelz VA
PROVIDER: S-EPMC4423764 | biostudies-literature | 2009
REPOSITORIES: biostudies-literature
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 20090101
We present a new multiscale method that combines all-atom molecular dynamics with coarse-grained sampling, towards the aim of bridging two levels of physiology: the atomic scale of protein side chains and small molecules, and the huge scale of macromolecular complexes like the ribosome. Our approach uses all-atom simulations of peptide (or other ligand) fragments to calculate local 3D spatial potentials of mean force (PMF). The individual fragment PMFs are then used as a potential for a coarse-g ...[more]