Module: sasa
| Description | Usage |
|---|---|
| Solvent Accessible Surface Area collective variable (SASA) | |
| Authors: Andrea Arsiccio |   |
Details
This SASA module contains methods for the calculation of the solvent accessible surface area (SASA) of proteins using either the fast algorithm by Hasel et al. that is described in the first paper cited below the LCPO algorithm that is described in the second paper. This module can be used to include the SASA as a collective variable in metadynamics simulations, and also for implicit solvent simulations as described in the last three papers cited below.
Installation
This module is not installed by default. Add --enable-modules=sasa to your './configure' command when building PLUMED to enable these features.
Actions
The following actions are part of this module
| Name | Description | Tags |
|---|---|---|
| SASA_HASEL | Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. | COLVAR |
| SASA_LCPO | Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it. | COLVAR |
References
More information about this module is available in the following articles:
- W. Hasel, T. F. Hendrickson, W. C. Still, A rapid approximation to the solvent accessible surface areas of atoms. Tetrahedron Computer Methodology. 1, 103–116 (1988)
- J. Weiser, P. S. Shenkin, W. C. Still, Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO). Journal of Computational Chemistry. 20, 217–230 (1999)
- A. Arsiccio, P. Ganguly, J.-E. Shea, A Transfer Free Energy Based Implicit Solvent Model for Protein Simulations in Solvent Mixtures: Urea-Induced Denaturation as a Case Study. The Journal of Physical Chemistry B. 126, 4472–4482 (2022)
- A. Arsiccio, J.-E. Shea, Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach. The Journal of Physical Chemistry B. 125, 5222–5232 (2021)
- A. Arsiccio, J.-E. Shea, Pressure Unfolding of Proteins: New Insights into the Role of Bound Water. The Journal of Physical Chemistry B. 125, 8431–8442 (2021)