(Q38698755)

5 September 2017

The free energy landscape of pseudorotation in 3'-5' and 2'-5' linked nucleic acids (English)

1 reference

5 September 2017

1 reference

2

Jack W Szostak

1 reference

5 September 2017

Li Li

1

1 reference

PMC publication ID

3982932

5 September 2017

language of work or name

English

0 references

publication date

5 February 2014

1 reference

Journal of the American Chemical Society

5 September 2017

1 reference

5 September 2017

136

1 reference

5 September 2017

7

1 reference

5 September 2017

2858-2865

1 reference

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

5 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Structural insights into the effects of 2'-5' linkages on the RNA duplex

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Scalable molecular dynamics with NAMD

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Perspective on the reactions between F- and CH3CH2F: the free energy landscape of the E2 and SN2 reaction channels

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Flexible docking in solution using metadynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Escaping free-energy minima

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3'-->2') oligonucleotide system

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Chemical etiology of nucleic acid structure

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

VMD: visual molecular dynamics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Nuclear magnetic resonance study of the molecular conformation of .beta.-pseudouridine in aqueous solution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Structural and energetic properties of the potential HIV-1 reverse transcriptase inhibitors d4A and d4G: a comprehensive theoretical investigation

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Extensive backbone dynamics in the GCAA RNA tetraloop analyzed using 13C NMR spin relaxation and specific isotope labeling

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Solution structure of an unusually stable RNA hairpin, 5GGAC(UUCG)GUCC

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

23 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Energetics of ion conduction through the K+ channel

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

NMR structure of a 2',5' RNA favors A type duplex with compact C2'endo nucleotide repeat

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Toward a Full Characterization of Nucleic Acid Components in Aqueous Solution: Simulations of Nucleosides

31 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

Free Energy Landscape of A-DNA to B-DNA Conversion in Aqueous Solution

3 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3982932

The crystal structure of guanosine dihydrate and inosine dihydrate

3 December 2018

1 reference

12 December 2020

Optimized free energies from bidirectional single-molecule force spectroscopy

1 reference

12 December 2020

Conformational properties of branched RNA fragments in aqueous solution

1 reference

12 December 2020

Conformational analysis of the sugar ring in nucleosides and nucleotides. New description using the concept of pseudorotation

1 reference

12 December 2020

Constant pressure molecular dynamics simulation: The Langevin piston method

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JA412079B

The eightfold path to non-enzymatic RNA replication

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JA412079B

Origin of life: The RNA world

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JA412079B

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JA412079B

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1021/JA412079B

Identifiers

DOI

10.1021/JA412079B

1 reference

5 September 2017

1 reference

PMC publication ID

3982932

5 September 2017

PubMed publication ID

24499340

1 reference

PMC publication ID

3982932