Recent advances in implicit solvent-based methods for biomolecular simulations (Q36662616)

15 August 2017

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title

Recent advances in implicit solvent-based methods for biomolecular simulations (English)

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15 August 2017

2

Charles L Brooks

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15 August 2017

Jianhan Chen

1

1 reference

PMC publication ID

2386893

15 August 2017

Jana Khandogin

series ordinal

3

1 reference

15 August 2017

4 March 2008

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Current Opinion in Structural Biology

15 August 2017

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15 August 2017

18

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15 August 2017

2

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15 August 2017

140-148

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Generalized Born model with a simple, robust molecular volume correction

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Linking folding with aggregation in Alzheimer's beta-amyloid peptides

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Polarizable atomic multipole solutes in a Poisson-Boltzmann continuum

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Can molecular dynamics simulations provide high-resolution refinement of protein structure?

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Hydrophobic cooperativity as a mechanism for amyloid nucleation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Computational sidechain placement and protein mutagenesis with implicit solvent models.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Order N algorithm for computation of electrostatic interactions in biomolecular systems

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Exploring atomistic details of pH-dependent peptide folding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Toward the accurate first-principles prediction of ionization equilibria in proteins.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

A residue-pairwise generalized born scheme suitable for protein design calculations.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Electrostatics calculations: latest methodological advances

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Interfaces and the driving force of hydrophobic assembly

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Folding cooperativity in a three-stranded beta-sheet model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Long dynamics simulations of proteins using atomistic force fields and a continuum representation of solvent effects: calculation of structural and dynamic properties

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Constant pH molecular dynamics with proton tautomerism

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Biomolecular simulations at constant pH.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Improving implicit solvent simulations: a Poisson-centric view

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Comparative study of generalized Born models: protein dynamics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Evaluation of a fast implicit solvent model for molecular dynamics simulations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Electrostatics of ligand binding: parametrization of the generalized Born model and comparison with the Poisson-Boltzmann approach

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

What role do surfaces play in GB models? A new-generation of surface-generalized born model based on a novel gaussian surface for biomolecules

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Acidic range titration of HEWL using a constant-pH molecular dynamics method.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

FACTS: Fast analytical continuum treatment of solvation.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Ab initio folding of albumin binding domain from all-atom molecular dynamics simulation

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

GBr(6): a parameterization-free, accurate, analytical generalized born method.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Analytical electrostatics for biomolecules: beyond the generalized Born approximation

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Incorporating variable dielectric environments into the generalized Born model

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Implicit solvent simulations of peptide interactions with anionic lipid membranes

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Refinement of NMR structures using implicit solvent and advanced sampling techniques

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Constant pH molecular dynamics in generalized Born implicit solvent

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

An electrostatic basis for the stability of thermophilic proteins

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Implicit solvation based on generalized Born theory in different dielectric environments

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

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

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Simulating proteins at constant pH: An approach combining molecular dynamics and Monte Carlo simulation.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2386893

Constant-pH molecular dynamics using continuous titration coordinates

20 October 2018

1 reference

12 December 2020

Free energy surfaces of miniproteins with a betabetaalpha motif: replica exchange molecular dynamics simulation with an implicit solvation model

1 reference

12 December 2020

Coupling hydrophobicity, dispersion, and electrostatics in continuum solvent models

1 reference

12 December 2020

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study

1 reference

12 December 2020

Direct folding simulation of alpha-helices and beta-hairpins based on a single all-atom force field with an implicit solvation model

1 reference

12 December 2020

Comparison of solvation-effect methods for the simulation of peptide interactions with a hydrophobic surface

1 reference

12 December 2020

Molecular simulation with variable protonation states at constant pH

1 reference

12 December 2020

Investigation of Salt Bridge Stability in a Generalized Born Solvent Model.

1 reference

12 December 2020

Efficient Generalized Born Models for Monte Carlo Simulations.

1 reference

12 December 2020

Assessment of Detection and Refinement Strategies for de novo Protein Structures Using Force Field and Statistical Potentials

1 reference

12 December 2020

10.1016/J.SBI.2008.01.003

Identifiers

DOI

1 reference

15 August 2017

1 reference

PMC publication ID

2386893

15 August 2017

PubMed publication ID

18304802

1 reference

PMC publication ID

2386893