Tailoring the variational implicit solvent method for new challenges: biomolecular recognition and assembly
Abstract: Predicting solvation free energies and describing the complex water behavior that plays an important role in essentially all biological processes is a major challenge from the computational standpoint. While an atomistic, explicit description of the solvent can turn out to be too expensive in large biomolecular systems, most implicit solvent methods fail to capture “dewetting” effects and heterogeneous hydration by relying on a pre-established (i.e., guessed) solvation interface. Here we focus on the Variational Implicit Solvent Method, an implicit solvent method that adds water “plasticity” back to the picture by formulating the solvation free energy as a functional of all possible solvation interfaces. We survey VISM's applications to the problem of molecular recognition and report some of the most recent efforts to tailor VISM for more challenging scenarios, with the ultimate goal of including thermal fluctuations into the framework. The advances reported herein pave the way to make VISM a uniquely successful approach to characterize complex solvation properties in the recognition and binding of large-scale biomolecular complexes
- Location
-
Deutsche Nationalbibliothek Frankfurt am Main
- Extent
-
Online-Ressource
- Language
-
Englisch
- Notes
-
Frontiers in molecular biosciences. - 12 (2018) , 00013, ISSN: 2296-889X
- Event
-
Veröffentlichung
- (where)
-
Freiburg
- (who)
-
Universität
- (when)
-
2022
- Creator
- Contributor
-
Applied Theoretical Physics - Computational Physics
- DOI
-
10.3389/fmolb.2018.00013/full
- URN
-
urn:nbn:de:bsz:25-freidok-2308652
- Rights
-
Open Access; Der Zugriff auf das Objekt ist unbeschränkt möglich.
- Last update
-
15.08.2025, 7:25 AM CEST
Data provider
Deutsche Nationalbibliothek. If you have any questions about the object, please contact the data provider.
Associated
- Ricci, Clarisse G.
- Li, Bo
- Cheng, Li-Tien
- Dzubiella, Joachim
- McCammon, J. Andrew
- Applied Theoretical Physics - Computational Physics
- Universität
Time of origin
- 2022
Other Objects (12)
An Implicit Solvent Model for Biomolecular Monte Carlo Simulations
Implicit optimal variational collaborative filtering
Fluid density approximation for an implicit solvent model
Stability Analysis for Parameterized Variational Systems with Implicit Constraints
Interacting with the biomolecular solvent accessible surface via a haptic feedback device
Variational symplectic diagonally implicit Runge-Kutta methods for isospectral systems
Systematic Selection and Tailoring of Biphasic Solvent Systems in Liquid-liquid Chromatography
Implicit-solvent coarse-grained simulations of linear-dendritic block copolymer micelles
An iterative algorithm for a system of generalized implicit variational inclusions
On Mann implicit composite subgradient extragradient methods for general systems of variational inequalities with hierarchical variational inequality constraints
Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent
Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
An Implicit Solvent Model for Biomolecular Monte Carlo Simulations
Implicit optimal variational collaborative filtering
Fluid density approximation for an implicit solvent model
Stability Analysis for Parameterized Variational Systems with Implicit Constraints
Interacting with the biomolecular solvent accessible surface via a haptic feedback device
Variational symplectic diagonally implicit Runge-Kutta methods for isospectral systems
Systematic Selection and Tailoring of Biphasic Solvent Systems in Liquid-liquid Chromatography
Implicit-solvent coarse-grained simulations of linear-dendritic block copolymer micelles
An iterative algorithm for a system of generalized implicit variational inclusions
On Mann implicit composite subgradient extragradient methods for general systems of variational inequalities with hierarchical variational inequality constraints
Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent
Modeling and computation of heterogeneous implicit solvent and its applications for biomolecules
An Implicit Solvent Model for Biomolecular Monte Carlo Simulations
Implicit optimal variational collaborative filtering
Fluid density approximation for an implicit solvent model
Stability Analysis for Parameterized Variational Systems with Implicit Constraints
Interacting with the biomolecular solvent accessible surface via a haptic feedback device
Variational symplectic diagonally implicit Runge-Kutta methods for isospectral systems
Systematic Selection and Tailoring of Biphasic Solvent Systems in Liquid-liquid Chromatography
Implicit-solvent coarse-grained simulations of linear-dendritic block copolymer micelles
An iterative algorithm for a system of generalized implicit variational inclusions
On Mann implicit composite subgradient extragradient methods for general systems of variational inequalities with hierarchical variational inequality constraints
Assessing RNA atomistic force fields via energy landscape explorations in implicit solvent