Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine (Q42086540)

16 October 2017

Base flip in DNA studied by molecular dynamics simulationsof differently-oxidized forms of methyl-Cytosine (English)

1 reference

16 October 2017

3

Petra Imhof

1 reference

16 October 2017

Mahdi Bagherpoor Helabad

series ordinal

1

object named as

Mahdi Bagherpoor Helabad

1 reference

16 October 2017

Natalia Kanaan

2

1 reference

16 October 2017

language of work or name

English

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publication date

3 July 2014

1 reference

International Journal of Molecular Sciences

16 October 2017

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16 October 2017

15

1 reference

16 October 2017

7

1 reference

16 October 2017

11799-11816

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Creative Commons Attribution 4.0 International

16 October 2017

start time

3 July 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

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Divergent mechanisms for enzymatic excision of 5-formylcytosine and 5-carboxylcytosine from DNA.

30 May 2018

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Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα-DNA recognition complex.

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Activity and crystal structure of human thymine DNA glycosylase mutant N140A with 5-carboxylcytosine DNA at low pH

30 May 2018

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The effect of a G:T mispair on the dynamics of DNA

30 May 2018

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

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

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Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation

30 May 2018

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

30 May 2018

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Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites

30 May 2018

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Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA

30 May 2018

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Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs

30 May 2018

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Base Flipping Free Energy Profiles for Damaged and Undamaged DNA

30 May 2018

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Detection of damaged DNA bases by DNA glycosylase enzymes

30 May 2018

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A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

30 May 2018

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Conformational analysis of nucleic acids revisited: Curves

30 May 2018

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

30 May 2018

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Central base pair flipping and discrimination by PspGI.

30 May 2018

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A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT

30 May 2018

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Recent advances in the study of nucleic acid flexibility by molecular dynamics

30 May 2018

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DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics

30 May 2018

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Extrahelical damaged base recognition by DNA glycosylase enzymes

30 May 2018

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A molecular dynamics study of slow base flipping in DNA using conformational flooding

30 May 2018

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Minor groove deformability of DNA: a molecular dynamics free energy simulation study

30 May 2018

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Computational approaches for investigating base flipping in oligonucleotides

30 May 2018

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GROMACS: fast, flexible, and free

30 May 2018

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Atomistic view of base flipping in DNA.

30 May 2018

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Simulation and modeling of nucleic acid structure, dynamics and interactions

30 May 2018

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30 May 2018

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Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

30 May 2018

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Synthesis and properties of oligonucleotides containing 5-formyl-2'-deoxycytidine: in vitro DNA polymerase reactions on DNA templates containing 5-formyl-2'-deoxycytidine

30 May 2018

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VMD: visual molecular dynamics

30 May 2018

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30 May 2018

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30 May 2018

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The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

30 May 2018

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Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139815

Adaptive biasing force method for scalar and vector free energy calculations

17 August 2018

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Magnitude and direction of DNA bending induced by screw-axis orientation: influence of sequence, mismatches and abasic sites

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139815

Exploring the free-energy landscape of a short peptide using an average force

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139815

DNA binding and nucleotide flipping by the human DNA repair protein AGT.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139815

Mutagenicity of 5-formylcytosine, an oxidation product of 5-methylcytosine, in DNA in mammalian cells

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139815

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139815

Base analog and neighboring base effects on substrate specificity of recombinant human G:T mismatch-specific thymine DNA-glycosylase.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4139815

Comparison of simple potential functions for simulating liquid water

17 August 2018

1 reference

https://api.crossref.org/works/10.3390/IJMS150711799

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/IJMS150711799

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/IJMS150711799

Specificity in Protein–DNA Interactions: Energetic Recognition by the (Cytosine-C5)-methyltransferase from HhaI

21 January 2018

1 reference

https://api.crossref.org/works/10.3390/IJMS150711799

21 January 2018

Identifiers

DOI

10.3390/IJMS150711799

1 reference

16 October 2017

1 reference

16 October 2017

PubMed publication ID

24995694

1 reference