Importance of explicit salt ions for protein stability in molecular dynamics simulation. (Q30430766)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9635744%20AND%20SRC:MED&resulttype=core&format=json

12 November 2019

title

Importance of explicit salt ions for protein stability in molecular dynamics simulation (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9635744%20AND%20SRC:MED&resulttype=core&format=json

molecular dynamics simulation

12 November 2019

main subject

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author

Rebecca C Wade

series ordinal

2

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12 November 2019

author name string

Ibragimova GT

series ordinal

1

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12 November 2019

language of work or name

English

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publication date

1 June 1998

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12 November 2019

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12 November 2019

volume

74

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12 November 2019

issue

6

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12 November 2019

page(s)

2906-2911

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A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

12 November 2019

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Insight into the stabilization of A-DNA by specific ion association: spontaneous B-DNA to A-DNA transitions observed in molecular dynamics simulations of d[ACCCGCGGGT]2 in the presence of hexaamminecobalt(III).

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Effect of periodic box size on aqueous molecular dynamics simulation of a DNA dodecamer with particle-mesh Ewald method

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Positioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Structure of the WW domain of a kinase-associated protein complexed with a proline-rich peptide.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

The WW domain of Yes-associated protein binds a proline-rich ligand that differs from the consensus established for Src homology 3-binding modules

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Molecular dynamics simulations of rubredoxin from Clostridium pasteurianum: changes in structure and electrostatic potential during redox reactions

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Atomic-level accuracy in simulations of large protein crystals

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

The effects of truncating long-range forces on protein dynamics.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Molecular dynamics study of the structure and dynamics of a protein molecule in a crystalline ionic environment, Streptomyces griseus protease A.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Cutoff size does strongly influence molecular dynamics results on solvated polypeptides

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

Structure and function of the WW domain.

20 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

The application of different solvation and electrostatic models in molecular dynamics simulations of ubiquitin: how well is the X-ray structure "maintained"?

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

WW domains and retrovirus budding

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1299631

RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin

26 November 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

Molecular dynamics with coupling to an external bath

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

Effect of warmup protocol and sampling time on convergence of molecular dynamics simulations of a DNA dodecamer using AMBER 4.1 and particle-mesh Ewald method

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

Molecular dynamics simulations of poly(dA).poly(dT): comparisons between implicit and explicit solvent representations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

An all atom force field for simulations of proteins and nucleic acids

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2898%2977997-4

10.1016/S0006-3495(98)77997-4

7 January 2021

Identifiers

DOI

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9635744%20AND%20SRC:MED&resulttype=core&format=json

12 November 2019

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https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:9635744%20AND%20SRC:MED&resulttype=core&format=json

12 November 2019

PubMed publication ID

9635744

1 reference