|
| A non-equilibrium method based on path optimization for predicting free energy |
| Received:September 24, 2009 Revised:January 18, 2010 |
| View Full Text View/Add Comment Download reader |
| DOI：10.7511/jslx20106001 |
| KeyWord:steered molecular dynamics genetic algorithm information entropy potentials of mean force dissociation free energy |
| Author | Institution |
| 杨坤 |
大连理工大学 工程力学系,大连理工大学工业装备结构分析国家重点实验室,大连 |
| 王希诚 |
大连理工大学 工程力学系,大连理工大学工业装备结构分析国家重点实验室,大连 |
|
| Hits: 2247 |
| Download times: 1698 |
| Abstract: |
| A non-equilibrium method based on path optimization for predicting free energy is developed in this paper. A multi-objective optimization model for unbinding protein-ligand complexes is constructed to obtain an optimal dissociation pathway with less dissociation time and lower energy consumption by using steered molecular dynamics. The unbinding free energy is then calculated along the optimal unbinding pathways. Comparing with Jarzynski extrapolation method based on potentials of mean force (PMF), the method has higher prediction efficiency. Comparisons of prediction accuracy with the experimental values are also given by numerical examples. The novel method can also simulate whole unbinding proceeding and give some important structural information for designing new drugs. |