Ontology highlight
ABSTRACT:
SUBMITTER: Ramakrishnan V
PROVIDER: S-EPMC3277656 | biostudies-literature | 2012 Mar
REPOSITORIES: biostudies-literature
Ramakrishnan Vibin V Srinivasan Sai Praveen SP Salem Saeed M SM Matthews Suzanne J SJ Colón Wilfredo W Zaki Mohammed M Bystroff Christopher C
Proteins 20111221 3
Protein unfolding is modeled as an ensemble of pathways, where each step in each pathway is the addition of one topologically possible conformational degree of freedom. Starting with a known protein structure, GeoFold hierarchically partitions (cuts) the native structure into substructures using revolute joints and translations. The energy of each cut and its activation barrier are calculated using buried solvent accessible surface area, side chain entropy, hydrogen bonding, buried cavities, and ...[more]