Abstract
We performed "weighted ensemble" path-sampling simulations of adenylate kinase, using several semiatomistic protein models. The models have an all-atom backbone with various levels of residue interactions. The primary result is that full statistically rigorous path sampling required only a few weeks of single-processor computing time with these models, indicating the addition of further chemical detail should be readily feasible. Our semiatomistic path ensembles are consistent with previous biophysical findings: the presence of two distinct pathways, identification of intermediates, and symmetry of forward and reverse pathways.
Original language | English (US) |
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Pages (from-to) | 3527-3539 |
Number of pages | 13 |
Journal | Journal of Chemical Theory and Computation |
Volume | 6 |
Issue number | 11 |
DOIs | |
State | Published - Nov 9 2010 |
Externally published | Yes |
ASJC Scopus subject areas
- Computer Science Applications
- Physical and Theoretical Chemistry