(Q37163939)

18 August 2017

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

1 reference

18 August 2017

8

Gregory A Voth

1 reference

18 August 2017

7

Hans C Andersen

1 reference

18 August 2017

W G Noid

1

1 reference

18 August 2017

Pu Liu

2

1 reference

18 August 2017

Yanting Wang

3

1 reference

18 August 2017

Jhih-Wei Chu

4

1 reference

18 August 2017

Gary S Ayton

5

1 reference

18 August 2017

Sergei Izvekov

6

1 reference

18 August 2017

language of work or name

English

0 references

publication date

1 June 2008

1 reference

Journal of Chemical Physics

18 August 2017

1 reference

18 August 2017

128

1 reference

18 August 2017

24

1 reference

18 August 2017

244115

1 reference

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

18 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Coarse-grained peptide modeling using a systematic multiscale approach

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

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=2671180

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=2671180

A natural coarse graining for simulating large biomolecular motion

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Coarse grained protein-lipid model with application to lipoprotein particles

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Toward understanding the dynamics of membrane-raft-based molecular interactions

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

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=2671180

Transmembrane peptide-induced lipid sorting and mechanism of Lalpha-to-inverted phase transition using coarse-grain 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=2671180

Orientational potentials extracted from protein structures improve native fold recognition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Molecular dynamics simulations of biomolecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Modeling the lipid component of membranes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Room-Temperature Ionic Liquids. Solvents for Synthesis and Catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Lipid rafts and signal transduction

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

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=2671180

Computer 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=2671180

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=2671180

Chemistry. Ionic liquids--solvents of the future?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Structure-derived potentials and protein simulations

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Multiscale coarse-graining of monosaccharides.

27 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Smart resolution replica exchange: an efficient algorithm for exploring complex energy landscapes.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Modeling real dynamics in the coarse-grained representation of condensed phase systems.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Multiscale coarse-graining of ionic liquids.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Optimal combination of theory and experiment for the characterization of the protein folding landscape of S6: how far can a minimalist model go?

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Optimizing physical energy functions for protein folding.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Assembly and analysis of conical models for the HIV-1 core.

3 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2671180

Complementary Matching in Domain Formation within Lipid Bilayers

3 September 2018

1 reference

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

21 January 2018

1 reference

Multiscale coarse graining of liquid-state systems

21 January 2018

1 reference

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

21 January 2018

1 reference

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

21 January 2018

1 reference

21 January 2018

1 reference

Equation-free: The computer-aided analysis of complex multiscale systems

21 January 2018

1 reference

Anisotropic coarse-grained statistical potentials improve the ability to identify nativelike protein structures

21 January 2018

1 reference

Unique spatial heterogeneity in ionic liquids

21 January 2018

1 reference

12 December 2020

The Mechanism of Vesicle Fusion as Revealed by Molecular Dynamics Simulations

1 reference

12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

Systematic coarse-graining of nanoparticle interactions in molecular dynamics simulation

1 reference

12 December 2020

Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel

1 reference

12 December 2020

Are many-body electronic polarization effects important in liquid water?

1 reference

12 December 2020

A macromolecule in a solvent: adaptive resolution molecular dynamics simulation

1 reference

12 December 2020

Multiscale Coarse-Graining of Mixed Phospholipid/Cholesterol Bilayers

1 reference

12 December 2020

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

1 reference

12 December 2020

Identifiers

DOI

10.1063/1.2938857

1 reference

18 August 2017

1 reference

18 August 2017

1 reference