Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex (Q34175734)

31 July 2017

Molecular dynamics and binding specificity analysis of the bovine immunodeficiency virus BIV Tat-TAR complex (English)

1 reference

Bovine immunodeficiency virus

31 July 2017

object named as

bovine immunodeficiency virus

1 reference

C M Reyes

1

1 reference

31 July 2017

R Nifosì

series ordinal

2

1 reference

31 July 2017

A D Frankel

series ordinal

3

1 reference

31 July 2017

P A Kollman

series ordinal

4

1 reference

31 July 2017

language of work or name

English

0 references

publication date

1 June 2001

1 reference

31 July 2017

10

1 reference

based on heuristic

inferred from page(s)

published in

Biophysical Journal

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31 July 2017

80

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31 July 2017

6

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31 July 2017

2833-2842

1 reference

Molecular dynamics studies of the HIV-1 TAR and its complex with argininamide

31 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Fitting peptides into the RNA world

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Structure and thermodynamics of RNA-protein binding: using molecular dynamics and free energy analyses to calculate the free energies of binding and conformational change

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Investigating the binding specificity of U1A-RNA by computational mutagenesis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Molecular dynamics and free-energy calculations applied to affinity maturation in antibody 48G7.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Biochemical and functional interactions between HIV-1 Tat protein and TAR RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Equine infectious anemia virus transactivator is a homeodomain-type protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Reduced surface: an efficient way to compute molecular surfaces

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Aqueous solution structure of a hybrid lentiviral Tat peptide and a model of its interaction with HIV-1 TAR RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

How Tat targets TAR: structure of the BIV peptide-RNA complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Evaluation of the conformational free energies of loops in proteins.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Control of RNA initiation and elongation at the HIV-1 promoter

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Structural variety of arginine-rich RNA-binding peptides

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

A peptide interaction in the major groove of RNA resembles protein interactions in the minor groove of DNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Structural studies of HIV-1 Tat protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Role of RNA structure in arginine recognition of TAR RNA.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Equine infectious anemia virus Tat is a predominantly helical protein

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Aromatic-aromatic interaction: a mechanism of protein structure stabilization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Electrostatic interactions in macromolecules: theory and applications

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Arginine-mediated RNA recognition: the arginine fork.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Specific binding of arginine to TAR RNA

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Molecular dynamics studies of U1A-RNA complexes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1301468

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

28 October 2018

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976250-9

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%2801%2976250-9

Simulations of the dynamics at an RNA-protein interface

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976250-9

Comparison of simple potential functions for simulating liquid water

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976250-9

Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976250-9

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%2801%2976250-9

Continuum solvent studies of the stability of RNA hairpin loops and helices

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FS0006-3495%2801%2976250-9

10.1016/S0006-3495(01)76250-9

7 January 2021

Identifiers

DOI

1 reference

31 July 2017

1 reference

31 July 2017

1 reference