(Q35768246)

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Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects

scientific article published on 3 November 2006

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scholarly article

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects (English)

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

5

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Arieh Warshel

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

author name string

Peter Oelschlaeger

1

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

Marco Klahn

2

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

William A Beard

3

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

Samuel H Wilson

4

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

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publication date

3 November 2006

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

Journal of Molecular Biology

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Europe PubMed Central

PubMed publication ID

10 August 2017

366

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

2

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

687-701

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

Simulating the effect of DNA polymerase mutations on transition-state energetics and fidelity: evaluating amino acid group contribution and allosteric coupling for ionized residues in human pol beta

1 reference

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12 July 2018

Magnesium-induced assembly of a complete DNA polymerase catalytic complex.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Structure and mechanism of DNA polymerase Beta.

1 reference

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12 July 2018

Structure and mechanism of DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Computer simulations of protein functions: searching for the molecular origin of the replication fidelity of DNA polymerases

1 reference

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12 July 2018

Highly organized but pliant active site of DNA polymerase beta: compensatory mechanisms in mutant enzymes revealed by dynamics simulations and energy analyses.

1 reference

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12 July 2018

Molecular mechanisms of mammalian DNA repair and the DNA damage checkpoints

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Orchestration of cooperative events in DNA synthesis and repair mechanism unraveled by transition path sampling of DNA polymerase beta's closing

1 reference

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12 July 2018

Structure/function correlations of proteins using MM, QM/MM, and related approaches: methods, concepts, pitfalls, and current progress

1 reference

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12 July 2018

Computer simulation of the chemical catalysis of DNA polymerases: discriminating between alternative nucleotide insertion mechanisms for T7 DNA polymerase

1 reference

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12 July 2018

What are the dielectric "constants" of proteins and how to validate electrostatic models?

1 reference

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12 July 2018

Insight into the catalytic mechanism of DNA polymerase beta: structures of intermediate complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Geometry of metal-ligand interactions in proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Successful molecular dynamics simulation of the zinc-bound farnesyltransferase using the cationic dummy atom approach.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Crystal structures of human DNA polymerase beta complexed with gapped and nicked DNA: evidence for an induced fit mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

VMD: visual molecular dynamics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Structure-function analysis of the mammalian DNA polymerase beta active site: role of aspartic acid 256, arginine 254, and arginine 258 in nucleotidyl transfer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Crystal structure of rat DNA polymerase beta: evidence for a common polymerase mechanism

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

12 July 2018

Mismatch-specific thymine DNA glycosylase and DNA polymerase beta mediate the correction of G.T mispairs in nuclear extracts from human cells

1 reference

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12 July 2018

Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603

1 reference

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12 July 2018

Computer simulation of the initial proton transfer step in human carbonic anhydrase I

1 reference

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12 July 2018

Modeling domino effects in enzymes: molecular basis of the substrate specificity of the bacterial metallo-beta-lactamases IMP-1 and IMP-6.

1 reference

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25 September 2018

Insight into the mechanism of the IMP-1 metallo-beta-lactamase by molecular dynamics simulations

1 reference

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25 September 2018

Computer simulation studies of the fidelity of DNA polymerases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1859854

25 September 2018

Successful molecular dynamics simulation of two zinc complexes bridged by a hydroxide in phosphotriesterase using the cationic dummy atom method

1 reference

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25 September 2018

DNA polymerase beta: contributions of template-positioning and dNTP triphosphate-binding residues to catalysis and fidelity

1 reference

https://pubmed.ncbi.nlm.nih.gov/17174326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process

1 reference

https://pubmed.ncbi.nlm.nih.gov/17174326

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Zinc binding in proteins and solution: a simple but accurate nonbonded representation

1 reference

https://pubmed.ncbi.nlm.nih.gov/17174326

12 December 2020

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Serotype-selective, small-molecule inhibitors of the zinc endopeptidase of botulinum neurotoxin serotype A

1 reference

https://pubmed.ncbi.nlm.nih.gov/17174326

12 December 2020

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A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.JMB.2006.10.095

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10.1016/J.JMB.2006.10.095

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

release_k37sikmqonaqvgowmtav3b3ksm

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https://api.fatcat.wiki/v0/release/k37sikmqonaqvgowmtav3b3ksm

24 November 2022

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PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

10 August 2017

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