(Q34356303)

1 August 2017

title

YUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models (English)

1 reference

1 August 2017

Robert K Z Tan

1

1 reference

1 August 2017

Anton S Petrov

series ordinal

2

1 reference

1 August 2017

Stephen C Harvey

series ordinal

3

1 reference

1 August 2017

publication date

18 March 2006

1 reference

Journal of Chemical Theory and Computation

1 August 2017

published in

1 reference

1 August 2017

volume

2

1 reference

1 August 2017

issue

3

1 reference

1 August 2017

page(s)

529-540

1 reference

DNA organization and thermodynamics during viral packing

1 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Simulating movement of tRNA into the ribosome during decoding

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

RNAML: a standard syntax for exchanging RNA information.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Exploring three-dimensional structures of the HIV-1 RNA/tRNALys3 initiation complex

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Modeling large RNAs and ribonucleoprotein particles using molecular mechanics techniques

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

A quantitative model of the Escherichia coli 16 S RNA in the 30 S ribosomal subunit.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Molecular mechanics model of supercoiled DNA.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

The kinemage: A tool for scientific communication

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Dynamics of folded proteins

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Packaging double-helical DNA into viral capsids

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Investigation of viral DNA packaging using molecular mechanics models

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Conformational transitions using molecular dynamics with minimum biasing.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3404851

Molecular dynamics simulations of small DNA plasmids: effects of sequence and supercoiling on intramolecular motions

27 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844233

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Molecular modeling of closed circular DNA thermodynamic ensembles

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22844233

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT050323R

1 reference

1 August 2017

1 reference

1 August 2017

1 reference