(Q31012447)

16 November 2017

Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study (English)

1 reference

molecular dynamics simulation

16 November 2017

0 references

author name string

Yuguang Mu

series ordinal

1

1 reference

PMCID

1367046

16 November 2017

Gerhard Stock

series ordinal

2

1 reference

PMCID

1367046

16 November 2017

language of work or name

English

0 references

publication date

20 October 2005

1 reference

16 November 2017

1 reference

16 November 2017

90

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16 November 2017

2

1 reference

16 November 2017

391-399

1 reference

Structure and dynamics of an RNA tetraloop: a joint molecular dynamics and NMR study

16 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Hinge-like motions in RNA kink-turns: the role of the second a-minor motif and nominally unpaired bases

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Does water play a structural role in the folding of small nucleic acids?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Simulation and modeling of nucleic acid structure, dynamics and interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg2+-induced conformational stabilization

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Residual dipolar couplings in nucleic acid structure determination

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

28 July 2018

RNA-protein interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Molecular dynamics applied to nucleic acids

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Molecular dynamics simulation of nucleic acids

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Induced fit in RNA-protein recognition

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Strategies for the Design of Drugs Targeting RNA and RNA-Protein Complexes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

The NMR structure of the 5S rRNA E-domain–protein L25 complex shows preformed and induced recognition

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Reduced surface: an efficient way to compute molecular surfaces

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

The snRNP 15.5K protein folds its cognate K-turn RNA: a combined theoretical and biochemical study

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Structure-based drug design targeting an inactive RNA conformation: exploiting the flexibility of HIV-1 TAR RNA.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Experimental and computational studies of the G[UUCG]C RNA tetraloop.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Inhibition of gene expression in human cells through small molecule-RNA interactions

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Conformational analysis of single-base bulges in A-form DNA and RNA using a hierarchical approach and energetic evaluation with a continuum solvent model.

25 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1367046

Characterization of the solution conformations of unbound and Tat peptide-bound forms of HIV-1 TAR RNA

25 November 2018

1 reference

12 December 2020

A modified version of the Cornell et al. force field with improved sugar pucker phases and helical repeat

1 reference

12 December 2020

Conformation of the TAR RNA-Arginine Complex by NMR Spectroscopy

1 reference

12 December 2020

Molecular dynamics simulation studies of induced fit and conformational capture in U1A-RNA binding: do molecular substates code for specificity?

1 reference

12 December 2020

Aminoglycoside binding to the hammerhead ribozyme: a general model for the interaction of cationic antibiotics with RNA

1 reference

12 December 2020

Simulation of the structure and dynamics of nonhelical RNA motifs

1 reference

12 December 2020

RNA solvation: a molecular dynamics simulation perspective

1 reference

12 December 2020

10.1529/BIOPHYSJ.105.069559

Identifiers

DOI

1 reference

16 November 2017

1 reference

16 November 2017

1 reference

PMCID

1367046