(Q36711952)

15 August 2017

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors (English)

1 reference

15 August 2017

1 reference

Evan J Arthur

1

1 reference

15 August 2017

Charles L Brooks

series ordinal

2

1 reference

15 August 2017

language of work or name

1 reference

20 January 2016

1 reference

Journal of Computational Chemistry

15 August 2017

1 reference

15 August 2017

37

1 reference

15 August 2017

10

1 reference

15 August 2017

927-939

1 reference

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Effective Approximation of Molecular Volume Using Atom-Centered Dielectric Functions in Generalized Born 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=4801733

Multiscale modeling of a conditionally disordered pH-sensing chaperone.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Folding simulations for proteins with diverse topologies are accessible in days with a physics-based force field and 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=4801733

All-atom empirical potential for molecular modeling and dynamics studies of 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=4801733

Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Crowding induced collective hydration of biological macromolecules over extended distances

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

The AGBNP2 Implicit Solvation 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=4801733

CHARMM: the biomolecular simulation program

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

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=4801733

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=4801733

Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding 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=4801733

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=4801733

Scalable molecular dynamics with NAMD

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

The Amber biomolecular simulation programs

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

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=4801733

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in 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=4801733

Exploring protein native states and large-scale conformational changes with a modified generalized born 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=4801733

An Implicit Membrane Generalized Born Theory for the Study of Structure, Stability, and Interactions of Membrane 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=4801733

Generalized born models of macromolecular solvation effects

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Solution conformations and thermodynamics of structured peptides: molecular dynamics simulation with an implicit solvation 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=4801733

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

The role of solvent in protein folding and in aggregation.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Establishing effective simulation protocols for beta- and alpha/beta-peptides. III. Molecular mechanical model for acyclic beta-amino acids.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

FACTS: Fast analytical continuum treatment of solvation.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Generalized born model with a simple smoothing function.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Collective properties of hydration: long range and specificity of hydrophobic interactions.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Family of G protein alpha chains: amphipathic analysis and predicted structure of functional domains

5 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FJCC.24280

Semianalytical treatment of solvation for molecular mechanics and dynamics

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FJCC.24280

Focusing of electric fields in the active site of Cu-Zn superoxide dismutase: effects of ionic strength and amino-acid modification

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801733

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

20 October 2018

1 reference

Crossref

https://api.crossref.org/works/10.1002%2FJCC.24280

Theory and applications of the generalized Born solvation model in macromolecular simulations

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26786647

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Constant-pH molecular dynamics using continuous titration coordinates

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26786647

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Calculation of the electric potential in the active site cleft due to alpha-helix dipoles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26786647

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1002/JCC.24280

1 reference

15 August 2017

journals/jcc/ArthurB16

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 August 2017

PubMed publication ID

26786647

1 reference