An explicit-solvent conformation search method using open software
- Published
- Accepted
- Subject Areas
- Biophysics, Pharmacology, Computational Science
- Keywords
- conformation search, explicit solvent, cluster analysis, replica exchange molecular dynamics
- Copyright
- © 2016 Gaalswyk et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. An explicit-solvent conformation search method using open software. PeerJ Preprints 4:e1931v1 https://doi.org/10.7287/peerj.preprints.1931v1
Abstract
Computer modeling is a popular tool to identify the most-probable conformers of a molecule. Although the solvent can have a large effect on the stability of a conformation, many popular conformational search methods are only capable of describing molecules in the gas phase or with an implicit solvent model. We have developed a work-flow for performing a conformation search on explicitly-solvated molecules using open source software. This method uses replica exchange molecular dynamics to sample the conformational states of the molecule efficiently. Cluster analysis is used to identify the most probable conformations from the simulated trajectory. This work-flow was tested on drug molecules a-amanitin and cabergoline to illustrate its capabilities and effectiveness. The preferred conformations of these molecules in gas phase, implicit solvent, and explicit solvent are significantly different.
Author Comment
This is a submission to PeerJ for review.