Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex (Q40150469)

17 September 2017

Free energy calculations and molecular dynamics simulations of wild-type and variants of the DNA-EcoRI complex (English)

1 reference

17 September 2017

2

Nilsson L

1 reference

17 September 2017

Sen S

1

1 reference

PMCID

1300465

17 September 2017

language of work or name

English

0 references

publication date

1 October 1999

1 reference

17 September 2017

10

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based on heuristic

inferred from page(s)

published in

Biophysical Journal

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17 September 2017

77

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17 September 2017

4

1 reference

17 September 2017

1801-1810

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Structure, interaction, dynamics and solvent effects on the DNA-EcoRI complex in aqueous solution from molecular dynamics simulation

17 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Molecular dynamics simulation of cytochrome c3: studying the reduction processes using free energy calculations

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Facilitated distortion of the DNA site enhances EcoRI endonuclease-DNA recognition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Protein-DNA complexes: the cost of recognition

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Molecular recognition mediated by bound water. A mechanism for star activity of the restriction endonuclease EcoRI

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Structure of restriction endonuclease BamHI and its relationship to EcoRI.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Refinement of Eco RI endonuclease crystal structure: a revised protein chain tracing

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Salt effects on protein-DNA interactions. The lambda cI repressor and EcoRI endonuclease.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Free energy calculation on base specificity of drug--DNA interactions: application to daunomycin and acridine intercalation into DNA.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Hydrostatic pressure reverses osmotic pressure effects on the specificity of EcoRI-DNA interactions

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Site specific point mutation changes specificity: A molecular modeling study by free energy simulations and enzyme kinetics of the thermodynamics in ribonuclease T1 substrate interactions

4 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1300465

Calculation of the relative change in binding free energy of a protein-inhibitor complex

2 December 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977025-6

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977025-6

Structure, thermodynamics and cooperativity of the glucocorticoid receptor DNA-binding domain in complex with different response elements. Molecular dynamics simulation and free energy perturbation studies

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977025-6

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977025-6

All-atom empirical potential for molecular modeling and dynamics studies of proteins

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977025-6

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%2899%2977025-6

MOPAC: a semiempirical molecular orbital program

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977025-6

Five-stranded beta-sheet sandwiched with two alpha-helices: a structural link between restriction endonucleases EcoRI and EcoRV

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2899%2977025-6

10.1016/S0006-3495(99)77025-6

7 January 2021

Identifiers

DOI

1 reference

17 September 2017

1 reference

17 September 2017

1 reference

PMCID

1300465