(Q42538747)

1 November 2017

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

1 reference

1 November 2017

2

1 reference

1 November 2017

Alexey Savelyev

1

1 reference

PMC publication ID

2712212

1 November 2017

language of work or name

English

0 references

publication date

1 May 2009

1 reference

1 November 2017

1 reference

1 November 2017

96

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1 November 2017

10

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1 November 2017

4044-4052

1 reference

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

1 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Flexible histone tails in a new mesoscopic oligonucleosome model

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

The Amber biomolecular simulation programs

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Compensating bends in a 16-base-pair DNA oligomer containing a T(3)A(3) segment: A NMR study of global DNA curvature.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Ion motions in molecular dynamics simulations on DNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

DNA and its counterions: a molecular dynamics study

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

BALL--rapid software prototyping in computational molecular biology. Biochemicals Algorithms Library

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Canonical dynamics: Equilibrium phase-space distributions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Brownian dynamics of double-stranded DNA in periodic systems with discrete salt

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

A coarse grain model for DNA.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Multiscale modeling of nucleosome dynamics

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Polymer chain models of DNA and chromatin.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Deriving effective mesoscale potentials from atomistic simulations.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712212

Multiscale modeling of lipids and lipid bilayers

16 August 2018

1 reference

12 December 2020

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations

1 reference

12 December 2020

A multiscale coarse-graining method for biomolecular systems

1 reference

12 December 2020

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

1 reference

12 December 2020

10.1016/J.BPJ.2009.02.067

Identifiers

DOI

1 reference

1 November 2017

1 reference

PMC publication ID

2712212

1 November 2017

PubMed publication ID

19450476

1 reference

PMC publication ID

2712212