(Q33721314)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

title

An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies (English)

1 reference

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1 March 2020

3

1 reference

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1 March 2020

author name string

Kun Song

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Arthur J Campbell

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Carlos de Los Santos

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Arthur P Grollman

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

Carlos Simmerling

6

1 reference

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1 March 2020

publication date

9 October 2009

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

Journal of Chemical Theory and Computation

1 March 2020

published in

1 reference

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1 March 2020

volume

5

1 reference

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1 March 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

page(s)

3105-3113

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

Molecular mechanics parameters for the FapydG DNA lesion

1 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Computational approaches for investigating base flipping in oligonucleotides

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

The Amber biomolecular simulation programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

DNA lesion recognition by the bacterial repair enzyme MutM

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

HhaI methyltransferase flips its target base out of the DNA helix

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

The crystal structure of Haelll methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Molecular mechanical studies of DNA flexibility: coupled backbone torsion angles and base-pair openings

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Energetic and conformational aspects of A:T base-pair opening within the DNA double helix.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Computational analysis of the mode of binding of 8-oxoguanine to formamidopyrimidine-DNA glycosylase.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Sequence-dependent base pair opening in DNA double helix

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

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

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5442445

The opening of a single base without perturbations of neighboring nucleotides: a study on crystal B-DNA duplex d(CGCGAATTCGCG)2

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26609990

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5 . dC5, d(TATAT):d(ATATA), and dA5 . dT5 in the B and Z forms of DNA

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26609990

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/26609990

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1021/CT9001575

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:26609990%20AND%20SRC:MED&resulttype=core&format=json

1 March 2020

PubMed publication ID

26609990

1 reference