title: Conserve Water: A Method for the Analysis of Solvent in Molecular Dynamics.
abstract: Molecular dynamics with explicit solvent is favored for its ability to more correctly simulate aqueous biological processes and has become routine thanks to increasingly powerful computational resources. However, analysis techniques including Markov state models (MSMs) ignore solvent atoms and focus solely on solute coordinates despite solvent being implicated in myriad biological phenomena. We present a unified framework called "solvent-shells featurization" for including solvent degrees of freedom in analysis and show that this method produces better models. We apply this method to simulations of dewetting in the two-domain protein BphC to generate a predictive MSM and identify functional water molecules. Furthermore, the proposed methodology could be easily extended for building MSMs of any systems with indistinguishable components.
authors.affiliation: Department of Chemistry, ∥Department of Computer Science, and §Department of Structural Biology, Stanford University , Stanford, California 94305, United States.
authors.forename: Matthew P
authors.initials: MP
authors.lastname: Harrigan
authors.affiliation: Department of Chemistry, ∥Department of Computer Science, and §Department of Structural Biology, Stanford University , Stanford, California 94305, United States.
authors.forename: Diwakar
authors.initials: D
authors.lastname: Shukla
authors.affiliation: Department of Chemistry, ∥Department of Computer Science, and §Department of Structural Biology, Stanford University , Stanford, California 94305, United States.
authors.forename: Vijay S
authors.initials: VS
authors.lastname: Pande
mesh_terms: D007700:Kinetics; D056004:Molecular Dynamics Simulation; D012997:Solvents / Q000737:chemistry*; D014867:Water / Q000737:chemistry*
chemical_list: D012997:Solvents; D014867:Water