LS-VISM: A software package for analysis of biomolecular solvation

Zhou, Shenggao; Cheng, Li-Tien; Sun, Hua; Che, Jianwei; Dzubiella, Joachim; Li, Bo; McCammon, J. Andrew

doi:10.1002/jcc.23890

Cited by 20 publications

(32 citation statements)

References 88 publications

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“…The solvation of nonpolar CB [7] has been systematically studied by the deterministic level-set method in our previous works, 44,45,47 where we found a wet state and a dry state, cf. Fig.…”

Section: B Cucurbit[7]urilmentioning

confidence: 96%

“…Implemented with a robust level-set method, such a model is able to capture polymodal hydration states and provide qualitatively accurate estimates of solvation free energies. 29,30,[39][40][41][42][43][44][45][46][47] More precisely, in the VISM, one minimizes a macroscopic solvation free-energy functional of all possible solute-solvent interfaces to find stable, equilibrium biomolecular conformations that are often local minimizers of the functional as well as to determine the corresponding solvation free energies. The level-set method numerically implements this minimization process by moving an initially guessed surface with the "normal velocity" that is the VISM boundary force on the solute-solvent interface.…”

Section: Introductionmentioning

confidence: 99%

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Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

Zhou

Sun

Cheng

et al. 2016

The Journal of Chemical Physics

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Recent years have seen the initial success of a variational implicit-solvent model (VISM), implemented with a robust level-set method, in capturing efficiently different hydration states and providing quantitatively good estimation of solvation free energies of biomolecules. The level-set minimization of the VISM solvation free-energy functional of all possible solute-solvent interfaces or dielectric boundaries predicts an equilibrium biomolecular conformation that is often close to an initial guess. In this work, we develop a theory in the form of Langevin geometrical flow to incorporate solute-solvent interfacial fluctuations into the VISM. Such fluctuations are crucial to biomolecular conformational changes and binding process. We also develop a stochastic level-set method to numerically implement such a theory. We describe the interfacial fluctuation through the "normal velocity" that is the solute-solvent interfacial force, derive the corresponding stochastic level-set equation in the sense of Stratonovich so that the surface representation is independent of the choice of implicit function, and develop numerical techniques for solving such an equation and processing the numerical data. We apply our computational method to study the dewetting transition in the system of two hydrophobic plates and a hydrophobic cavity of a synthetic host molecule cucurbit [7]uril. Numerical simulations demonstrate that our approach can describe an underlying system jumping out of a local minimum of the free-energy functional and can capture dewetting transitions of hydrophobic systems. In the case of two hydrophobic plates, we find that the wavelength of interfacial fluctuations has a strong influence to the dewetting transition. In addition, we find that the estimated energy barrier of the dewetting transition scales quadratically with the inter-plate distance, agreeing well with existing studies of molecular dynamics simulations. Our work is a first step toward the inclusion of fluctuations into the VISM and understanding the impact of interfacial fluctuations on biomolecular solvation with an implicit-solvent approach. Published by AIP Publishing. [http://dx

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“…The solvation of nonpolar CB [7] has been systematically studied by the deterministic level-set method in our previous works, 44,45,47 where we found a wet state and a dry state, cf. Fig.…”

Section: B Cucurbit[7]urilmentioning

confidence: 96%

Section: Introductionmentioning

confidence: 99%

Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

Zhou

Sun

Cheng

et al. 2016

The Journal of Chemical Physics

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“…Programs have been developed to minimize user interventions in performing repetitive computational tasks and analyses, including D/I‐ASM calculations . The PHASEGO package determines phase boundaries and plots phase diagrams .…”

Section: Introductionmentioning

confidence: 99%

ExcelAutomat 1.3: Fragment analysis based on the distortion/interaction‐activation strain model

et al. 2018

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The distortion/interaction-activation strain model (D/I-ASM), a fragment analysis method, is applied to study the structure-reactivity relationship in reactions. The application of D/I-ASM involves the generation of input files for points along a reaction profile, submission of input files to a quantum software package, processing of parameters from the resulting output files and generation of graphical plots. The ExcelAutomat tool (Laloo et al., J. Comput. Aided Mol. Des. 2017, 31, 667) provides a framework and library in Visual Basic for Application programming language to process such files. New routines were written in ExcelAutomat 1.3 to facilitate processing of files for D/I-ASM. The worksheet "ASM" was included where initial parameters needed can be defined. The routines for D/I-ASM were tested successfully on bimolecular nucleophilic substitution, cycloaddition, and barrierless reactions. The automation of fragment analysis by ExcelAutomat 1.3 is compatible with Microsoft Excel and LibreOffice Calc. The extensible tool processes files from Gaussian and GAMESS-US packages.

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“…Refs. [61][62][63][64][65][66][67][68][69][70][71][72]. In general, stable equilibrium solute-solvent interfaces determined by the levelset VISM can be quite different from vdWS, SES, or SAS, particularly when it comes to the description of hydrophobic interactions.…”

Section: Introductionmentioning

confidence: 99%

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

Sun

Wen

Zhao³

et al. 2015

The Journal of Chemical Physics

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Dielectric boundary based implicit-solvent models provide efficient descriptions of coarse-grained effects, particularly the electrostatic effect, of aqueous solvent. Recent years have seen the initial success of a new such model, variational implicit-solvent model (VISM) McCammon Phys. Rev. Lett. 96, 087802 (2006) and J. Chem. Phys. 124, 084905 (2006)], in capturing multiple dry and wet hydration states, describing the subtle electrostatic effect in hydrophobic interactions, and providing qualitatively good estimates of solvation free energies. Here, we develop a phase-field VISM to the solvation of charged molecules in aqueous solvent to include more flexibility. In this approach, a stable equilibrium molecular system is described by a phase field that takes one constant value in the solute region and a different constant value in the solvent region, and smoothly changes its value on a thin transition layer representing a smeared solute-solvent interface or dielectric boundary. Such a phase field minimizes an effective solvation free-energy functional that consists of the solute-solvent interfacial energy, solute-solvent van der Waals interaction energy, and electrostatic free energy described by the Poisson-Boltzmann theory. We apply our model and methods to the solvation of single ions, two parallel plates, and protein complexes BphC and p53/MDM2 to demonstrate the capability and efficiency of our approach at different levels. With a diffuse dielectric boundary, our new approach can describe the dielectric asymmetry in the solute-solvent interfacial region. Our theory is developed based on rigorous mathematical studies and is also connected to the Lum-Chandler-Weeks theory (1999). We discuss these connections and possible extensions of our theory and methods. C 2015 AIP Publishing LLC. [http://dx

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LS-VISM: A software package for analysis of biomolecular solvation

Cited by 20 publications

References 88 publications

Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations

ExcelAutomat 1.3: Fragment analysis based on the distortion/interaction‐activation strain model

A self-consistent phase-field approach to implicit solvation of charged molecules with Poisson–Boltzmann electrostatics

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