Additive CHARMM force field for naturally occurring modified ribonucleotides (Q39290921)

10 September 2017

Additive CHARMM force field for naturally occurring modified ribonucleotides (English)

1 reference

10 September 2017

0 references

1 reference

2

1 reference

10 September 2017

Alexey Aleksandrov

3

0 references

Lennart Nilsson

object named as

Lennart Nilsson

series ordinal

5

0 references

author name string

You Xu

series ordinal

1

1 reference

PMCID

4801715

10 September 2017

Alexander D MacKerell

series ordinal

4

1 reference

10 September 2017

3 February 2016

1 reference

Journal of Computational Chemistry

10 September 2017

1 reference

10 September 2017

37

1 reference

10 September 2017

896-912

1 reference

10 September 2017

10

1 reference

Influence of Sequence and Covalent Modifications on Yeast tRNA Dynamics

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

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

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Lipid14: The Amber Lipid Force Field.

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

The contribution of pseudouridine to stabilities and structure of RNAs

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Posttranscriptional RNA Modifications: playing metabolic games in a cell's chemical Legoland

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Thermodynamic contribution and nearest-neighbor parameters of pseudouridine-adenosine base pairs in oligoribonucleotides

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Transfer RNA modifications: nature's combinatorial chemistry playground.

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Biosynthesis and function of posttranscriptional modifications of transfer RNAs

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Structure and function of noncanonical nucleobases

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Nucleotide modifications and tRNA anticodon-mRNA codon interactions on the ribosome

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

How mutations in tRNA distant from the anticodon affect the fidelity of decoding

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

The RNA Modification Database, RNAMDB: 2011 update

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Effect of pseudouridylation on the structure and activity of the catalytically essential P6.1 hairpin in human telomerase RNA

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

CHARMM: the biomolecular simulation program

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Additive empirical force field for hexopyranose monosaccharides

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Synthesis and solution conformation studies of 3-substituted uridine and pseudouridine derivatives

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

GLYCAM06: a generalizable biomolecular force field. Carbohydrates

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

tRNA's wobble decoding of the genome: 40 years of modification

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Molecular dynamics simulations of human tRNA Lys,3 UUU: the role of modified bases in mRNA recognition

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Comparison of multiple Amber force fields and development of improved protein backbone parameters

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Post-transcriptional nucleotide modification and alternative folding of RNA

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Empirical force fields for biological macromolecules: overview and issues.

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Development and testing of a general amber force field

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Investigation of Overhauser effects between pseudouridine and water protons in RNA helices

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Ab initio conformational analysis of nucleic acid components: intrinsic energetic contributions to nucleic acid structure and dynamics

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Methylation of the nucleobases in RNA oligonucleotides mediates duplex-hairpin conversion

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

The crystal structure of yeast phenylalanine tRNA at 1.93 A resolution: a classic structure revisited

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Pseudouridine in RNA: what, where, how, and why

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Effects of anticodon 2'-O-methylations on tRNA codon recognition in an Escherichia coli cell-free translation

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Stabilization of the anticodon stem-loop of tRNALys,3 by an A+-C base-pair and by pseudouridine

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Stabilizing effects of the RNA 2'-substituent: crystal structure of an oligodeoxynucleotide duplex containing 2'-O-methylated adenosines

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Structure of an RNA hairpin loop with a 5'-CGUUUCG-3' loop motif by heteronuclear NMR spectroscopy and distance geometry

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Solution structure of RNA duplexes containing alternating CG base pairs: NMR study of r(CGCGCG)2 and 2'-O-Me(CGCGCG)2 under low salt conditions

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Posttranscriptional modification of tRNA in psychrophilic bacteria

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Conformational flexibility in RNA: the role of dihydrouridine

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

The crystal structure of N4-methylcytosine.guanosine base-pairs in the synthetic hexanucleotide d(CGCGm4CG)

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

A novel guanine-guanine base pairing: crystal structure of a complex between 7-methylguanosine and its iodide

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

The 3 A crystal structure of yeast initiator tRNA: functional implications in initiator/elongator discrimination

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Conformational features of 2'-O-methyl-adenosylyl-adenosine

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Effect of temperature and protonation upon the conformation of . Correlation of conformational parameters in purine nucleosides

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding

10 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Structural and functional roles of the N1- and N3-protons of psi at tRNA's position 39

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Robustness in the fitting of molecular mechanics parameters.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Reparameterization of RNA chi Torsion Parameters for the AMBER Force Field and Comparison to NMR Spectra for Cytidine and Uridine.

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Stabilization of RNA stacking by pseudouridine

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

On the conformation of 5-substituted uridines as studied by proton magnetic resonance

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

NMR and CD studies on an oligonucleotide containing N4-methylcytosine

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Comparative structural analysis of 1-methyladenosine, 7-methylguanosine, ethenoadenosine and their protonated salts IV: 1H, 13C, and 15N NMR studies at natural isotope abundance

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Stacking-unstacking of the dinucleoside monophosphate guanylyl-3',5'-uridine studied with molecular dynamics

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Restricted rotation about the exocyclic carbon-nitrogen bond in cytosine derivatives

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Effects of methylation on the stability of nucleic acid conformations: studies at the monomer level.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Capping of eucaryotic mRNAs

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Conformation of N4-acetylcytidine, a modified nucleoside of tRNA, and stereochemistry of codon-anticodon interaction

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

A relation between inhibition of protein synthesis and conformation of 5′-phosphorylated 7-methylguanosine derivatives

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

A novel lysine-substituted nucleoside in the first position of the anticodon of minor isoleucine tRNA from Escherichia coli.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Rapid communication capturing the destabilizing effect of dihydrouridine through molecular simulations.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Backbone-base interactions critical to quantum stabilization of transfer RNA anticodon structure.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

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

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Effect of a water molecule on the sugar puckering of uridine, 2'-deoxyuridine, and 2'-O-methyl uridine inserted in duplexes

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Solution conformations of two naturally occurring RNA nucleosides: 3-methyluridine and 3-methylpseudouridine

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4801715

The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin.

21 August 2018

1 reference

An improved GROMOS96 force field for aliphatic hydrocarbons in the condensed phase

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

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

21 January 2018

1 reference

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

21 January 2018

1 reference

Conformational Preferences of Modified Uridines: Comparison of AMBER Derived Force Fields

21 January 2018

1 reference

Conformational Rigidity of N4-Acetyl-2′-O-methylcytidine Found in tRNA of Extremely Thermophilic Archaebacteria (Archaea)

21 January 2018

1 reference

Systematic ab initio gradient calculation of molecular geometries, force constants, and dipole moment derivatives

21 January 2018

1 reference

Hydrophobic Groups Stabilize the Hydration Shell of 2'-O-Methylated RNA Duplexes

21 January 2018

1 reference

12 December 2020

Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group

1 reference

12 December 2020

Molecular structure and vibrational spectra of N4-acetylcytosine

1 reference

12 December 2020

AMBER Force Field Parameters for the Naturally Occurring Modified Nucleosides in RNA

1 reference

12 December 2020

Base stacking of simple mRNA cap analogues. Association of 7,9-dimethylguanine, 7-methylguanosine and 7-methylguanosine 5'-monophosphate with indole and purine derivatives in aqueous solution

1 reference

12 December 2020

Optical studies of the base-stacking properties of 2'-O-methylated dinucleoside monophosphates

1 reference

12 December 2020

Tryptophan transfer RNA as the UGA suppressor

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

Stereochemistry of nucleic acids and their constituents. XXIII. Crystal and molecular structure of dihydrouridine "hemihydrate", a rare nucleoside with a saturated base occurring in the dihydrouridine loop of transfer ribonucleic acids

1 reference

12 December 2020

A Proton Magnetic Resonance Study of the Molecular Conformation of a Modified Nucleoside from Transfer RNA. Dihydrouridine

1 reference

12 December 2020

Comparative conformations of uridine and pseudouridine and their derivatives

1 reference

12 December 2020

Crystal structure of unmodified tRNA(Gln) complexed with glutaminyl-tRNA synthetase and ATP suggests a possible role for pseudo-uridines in stabilization of RNA structure

1 reference

12 December 2020

Nuclear magnetic resonance study of the impact of ribose 2'-O-methylation on the aqueous solution conformation of cytidylyl-(3' leads to 5')-cytidine

1 reference

12 December 2020

An RNA model system for investigation of pseudouridine stabilization of the codon-anticodon interaction in tRNALys, tRNAHis and tRNATyr

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.24307

1 reference

10 September 2017

journals/jcc/XuVAMN16

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

10 September 2017

1 reference

PMCID

4801715