Abstract
Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling e¿ciency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic
chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater e¿ciency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, o¿ering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.
chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater e¿ciency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, o¿ering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.
| Originalsprog | Engelsk |
|---|---|
| Tidsskrift | Journal of Chemical Theory and Computation |
| Vol/bind | 8 |
| Udgave nummer | 2 |
| Sider (fra-til) | 695-702 |
| Antal sider | 8 |
| ISSN | 1549-9618 |
| DOI | |
| Status | Udgivet - 14 feb. 2012 |