(Q38646397)

5 September 2017

Reference state for the generalized Yvon-Born-Green theory: application for coarse-grained model of hydrophobic hydration (English)

1 reference

5 September 2017

1 reference

J W Mullinax

1

1 reference

PMCID

3188631

5 September 2017

W G Noid

series ordinal

2

1 reference

PMCID

3188631

5 September 2017

language of work or name

English

0 references

publication date

1 September 2010

1 reference

Journal of Chemical Physics

5 September 2017

1 reference

5 September 2017

133

1 reference

5 September 2017

12

1 reference

5 September 2017

124107

1 reference

Recovering physical potentials from a model protein databank

5 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Coarse-grained potential models for phenyl-based molecules: I. Parametrization using experimental data

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

A Transferable Coarse Grain Non-bonded Interaction Model For Amino Acids.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Systematic coarse graining from structure using internal states: application to phospholipid/cholesterol bilayer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The multiscale coarse-graining method. IV. Transferring coarse-grained potentials between temperatures

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Multiscale modeling of emergent materials: biological and soft matter

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Evaluating the transferability of coarse-grained, density-dependent implicit solvent models to mixtures and chains

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Coarse-grained models of protein folding: toy models or predictive tools?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Multiscale simulation of soft matter: from scale bridging to adaptive resolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The MARTINI force field: coarse grained model for biomolecular simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Multiscale coarse-graining and structural correlations: connections to liquid-state theory

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Potential energy functions for protein design.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Multiscale modeling of biomolecular systems: in serial and in parallel

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

In quest of an empirical potential for protein structure prediction.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

GROMACS: fast, flexible, and free

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Implicit solvent simulation models for biomembranes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Coarse-grained models for proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Optimal prediction and the Mori-Zwanzig representation of irreversible processes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Canonical dynamics: Equilibrium phase-space distributions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Knowledge-based potentials for proteins

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

A computer model to dynamically simulate protein folding: studies with crambin.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

A simplified representation of protein conformations for rapid simulation of protein folding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

On the formation of protein tertiary structure on a computer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Structure-derived potentials and protein simulations

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Comparison of database potentials and molecular mechanics force fields

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Coarse-grained potential models for phenyl-based molecules: II. Application to fullerenes.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Analysis of knowledge-based protein-ligand potentials using a self-consistent method

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Calculation of conformational ensembles from potentials of mean force. An approach to the knowledge-based prediction of local structures in globular proteins.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The MARTINI Coarse-Grained Force Field: Extension to Proteins.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The multiscale coarse-graining method. V. Isothermal-isobaric ensemble

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Generalized Yvon-Born-Green theory for molecular systems.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Coarse-grained, density dependent implicit solvent model reliably reproduces behavior of a model surfactant system.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Note on the free energy of transfer of fullerene C60 simulated by using classical potentials.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Representability problems for coarse-grained water potentials.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

A physical reference state unifies the structure-derived potential of mean force for protein folding and binding.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Deriving effective mesoscale potentials from atomistic simulations.

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Statistical potentials extracted from protein structures: how accurate are they?

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3188631

Coarse-graining in polymer simulation: from the atomistic to the mesoscopic scale and back

31 August 2018

1 reference

Reverse Monte Carlo Simulation: A New Technique for the Determination of Disordered Structures

21 January 2018

1 reference

The inverse problem in classical statistical mechanics

21 January 2018

1 reference

Multiscale coarse graining of liquid-state systems

21 January 2018

1 reference

GROMACS 3.0: a package for molecular simulation and trajectory analysis

21 January 2018

1 reference

21 January 2018

1 reference

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

21 January 2018

1 reference

Structural modelling of glasses using reverse Monte Carlo simulation

21 January 2018

1 reference

A macromolecule in a solvent: adaptive resolution molecular dynamics simulation

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20886924

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

A multiscale coarse-graining method for biomolecular systems

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20886924

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Calculation of effective interaction potentials from radial distribution functions: A reverse Monte Carlo approach

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20886924

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1063/1.3481574

1 reference

5 September 2017

1 reference

5 September 2017

1 reference

PMCID

3188631