(Q35180754)

7 August 2017

title

Improved Generalized Born Solvent Model Parameters for Protein Simulations (English)

1 reference

7 August 2017

Hai Nguyen

1

1 reference

7 August 2017

Daniel R Roe

series ordinal

2

1 reference

7 August 2017

Carlos Simmerling

series ordinal

3

1 reference

7 August 2017

publication date

1 April 2013

1 reference

Journal of Chemical Theory and Computation

7 August 2017

published in

1 reference

7 August 2017

volume

9

1 reference

7 August 2017

issue

4

1 reference

7 August 2017

page(s)

2020-2034

1 reference

Single Stranded Loops of Quadruplex DNA As Key Benchmark for Testing Nucleic Acids Force Fields

7 August 2017

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Improving the description of salt bridge strength and geometry in a Generalized Born model

28 July 2018

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Generalized Born model with a simple, robust molecular volume correction

28 July 2018

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28 July 2018

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Microsecond simulations of the folding/unfolding thermodynamics of the Trp-cage miniprotein.

28 July 2018

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28 July 2018

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Computing the stability diagram of the Trp-cage miniprotein

28 July 2018

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A test on peptide stability of AMBER force fields with implicit solvation

28 July 2018

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Structural insights for designed alanine-rich helices: comparing NMR helicity measures and conformational ensembles from molecular dynamics simulation

28 July 2018

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MM-GB/SA rescoring of docking poses in structure-based lead optimization.

28 July 2018

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

28 July 2018

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Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction

28 July 2018

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

28 July 2018

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Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation

28 July 2018

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

28 July 2018

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28 July 2018

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

28 July 2018

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HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations

28 July 2018

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Folding cooperativity in a three-stranded beta-sheet model

28 July 2018

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High-resolution x-ray crystal structures of the villin headpiece subdomain, an ultrafast folding protein

28 July 2018

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Structural basis for coevolution of a human immunodeficiency virus type 1 nucleocapsid-p1 cleavage site with a V82A drug-resistant mutation in viral protease

28 July 2018

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Enhanced hairpin stability through loop design: the case of the protein G B1 domain hairpin

28 July 2018

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

28 July 2018

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

28 July 2018

1 reference

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Trp-cage: Folding free energy landscape in explicit water

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Free energy landscape of protein folding in water: Explicit vs. implicit solvent

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

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

28 July 2018

1 reference

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Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

28 July 2018

1 reference

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Understanding folding and design: replica-exchange simulations of "Trp-cage" miniproteins

28 July 2018

1 reference

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Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

28 July 2018

1 reference

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Designing a 20-residue protein

28 July 2018

1 reference

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Structure of tetragonal hen egg-white lysozyme at 0.94 A from crystals grown by the counter-diffusion method

28 July 2018

1 reference

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Tryptophan zippers: Stable, monomeric -hairpins

28 July 2018

1 reference

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NMR structure of the 35-residue villin headpiece subdomain

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Ligand binding alters the backbone mobility of intestinal fatty acid-binding protein as monitored by 15N NMR relaxation and 1H exchange

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Structure of ubiquitin refined at 1.8 A resolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Validation of Molecular Dynamics Simulations of Biomolecules Using NMR Spin Relaxation as Benchmarks: Application to the AMBER99SB Force Field.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

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

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

The AGBNP2 Implicit Solvation Model.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Balancing simulation accuracy and efficiency with the Amber united atom force field

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Evaluating the performance of the ff99SB force field based on NMR scalar coupling data

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Analysis of integral expressions for effective Born radii.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Incorporating variable dielectric environments into the generalized Born model

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Effective Born radii in the generalized Born approximation: the importance of being perfect

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Genetic algorithms: principles of natural selection applied to computation.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4361090

Quantitative Molecular Ensemble Interpretation of NMR Dipolar Couplings without Restraints

27 September 2018

1 reference

12 December 2020

Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models

1 reference

12 December 2020

Comparative study of generalized born models: Born radii and peptide folding

1 reference

12 December 2020

Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring

1 reference

12 December 2020

Identifiers

DOI

10.1021/CT3010485

1 reference

7 August 2017

1 reference

7 August 2017

1 reference