Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. (Q30367039)

21 June 2017

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title

Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. (English)

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21 June 2017

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Charles L Brooks

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21 June 2017

Jianhan Chen

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21 June 2017

language of work or name

English

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publication date

14 November 2007

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Physical Chemistry Chemical Physics

21 June 2017

published in

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21 June 2017

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21 June 2017

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21 June 2017

page(s)

471-481

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Peptide folding simulations

21 June 2017

cites work

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Progress in modeling of protein structures and interactions

21 January 2018

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Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet

21 January 2018

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Toward high-resolution de novo structure prediction for small proteins.

21 January 2018

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An all-atom force field for tertiary structure prediction of helical proteins

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The protein structure prediction problem could be solved using the current PDB library

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Progress over the first decade of CASP experiments.

21 January 2018

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Empirical force fields for biological macromolecules: overview and issues.

21 January 2018

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How well can simulation predict protein folding kinetics and thermodynamics?

21 January 2018

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

21 January 2018

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Recent advances in the development and application of implicit solvent models in biomolecule simulations

21 January 2018

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21 January 2018

Implicit solvent models

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Solvation energy in protein folding and binding

21 January 2018

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Evaluation of a fast implicit solvent model for molecular dynamics simulations

21 January 2018

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Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

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Generalized born models of macromolecular solvation effects

21 January 2018

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Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field

21 January 2018

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Exploring atomistic details of pH-dependent peptide folding

21 January 2018

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Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network

21 January 2018

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Generalized born model with a simple smoothing function.

21 January 2018

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Replica-exchange molecular dynamics method for protein folding

21 January 2018

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MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

21 January 2018

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Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions

21 January 2018

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Absolute comparison of simulated and experimental protein-folding dynamics

21 January 2018

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Influence of temperature, friction, and random forces on folding of the B-domain of staphylococcal protein A: all-atom molecular dynamics in implicit solvent.

21 January 2018

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Folding free-energy landscape of villin headpiece subdomain from molecular dynamics simulations

21 January 2018

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Improving implicit solvent simulations: a Poisson-centric view

21 January 2018

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Optimized Radii for Poisson-Boltzmann Calculations with the AMBER Force Field

21 January 2018

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Optimized atomic radii for protein continuum electrostatics solvation forces.

21 January 2018

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Interfaces and the driving force of hydrophobic assembly

21 January 2018

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Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics

21 January 2018

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Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides

21 January 2018

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Hydrophobic bonding and accessible surface area in proteins

21 January 2018

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Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water

21 January 2018

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Interfacial free energy and the hydrophobic effect

21 January 2018

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Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects

21 January 2018

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Exploring protein native states and large-scale conformational changes with a modified generalized born model

21 January 2018

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The interpretation of protein structures: Estimation of static accessibility

21 January 2018

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Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures

21 January 2018

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On the nonpolar hydration free energy of proteins: surface area and continuum solvent models for the solute-solvent interaction energy.

21 January 2018

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

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Comparison of simple potential functions for simulating liquid water

21 January 2018

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Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins

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Modeling Aromatic Liquids: Toluene, Phenol, and Pyridine.

21 January 2018

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NMR structure of the 35-residue villin headpiece subdomain

21 January 2018

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Three-dimensional solution structure of the B domain of staphylococcal protein A: comparisons of the solution and crystal structures

21 January 2018

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Improved treatment of the protein backbone in empirical force fields.

21 January 2018

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Two-stage folding of HP-35 from ab initio simulations

21 January 2018

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Temperature and length scale dependence of hydrophobic effects and their possible implications for protein folding.

21 January 2018

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The importance of solute-solvent van der Waals interactions with interior atoms of biopolymers

21 January 2018

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Assessing implicit models for nonpolar mean solvation forces: the importance of dispersion and volume terms

21 January 2018

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AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling.

21 January 2018

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Tryptophan zippers: Stable, monomeric -hairpins

21 January 2018

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Secondary-structure preferences of force fields for proteins evaluated by generalized-ensemble simulations

21 January 2018

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21 January 2018

Identifiers

DOI

10.1039/B714141F

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release_aybc7sq3vvdjvorgdx66cdqpmi

21 June 2017

Fatcat ID

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Fatcat

https://api.fatcat.wiki/v0/release/aybc7sq3vvdjvorgdx66cdqpmi

mapped directly with Wikidata item

24 November 2022

based on heuristic

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