The Mechanism of the Translocation Step in DNA Replication by DNA Polymerase I: A Computer Simulation Analysis (Q27659793)

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Direct observation of base-pair stepping by RNA polymerase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Processive DNA synthesis observed in a polymerase crystal suggests a mechanism for the prevention of frameshift mutations

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Structure of the replicating complex of a pol alpha family DNA polymerase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Crystal structure of a pol alpha family replication DNA polymerase from bacteriophage RB69

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

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

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Structures of mismatch replication errors observed in a DNA polymerase

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

DNA polymerases: structural diversity and common mechanisms

20 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Structure and mechanism of DNA polymerases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

DNA polymerase fidelity: kinetics, structure, and checkpoints

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Dependence of DNA polymerase replication rate on external forces: a model based on molecular dynamics simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Atomistic understanding of kinetic pathways for single base-pair binding and unbinding in DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Transition path sampling: throwing ropes over rough mountain passes, in the dark.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Conformational coupling in DNA polymerase fidelity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Function and structure relationships in DNA polymerases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

An attempt to unify the structure of polymerases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Pre-steady-state kinetic analysis of processive DNA replication including complete characterization of an exonuclease-deficient mutant

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Polymerase beta simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

A mutant of DNA polymerase I (Klenow fragment) with reduced fidelity

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

The structural mechanism of translocation and helicase activity in T7 RNA polymerase

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Computer simulation studies of the fidelity of DNA polymerases

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Fidelity of Escherichia coli DNA polymerase III holoenzyme. The effects of beta, gamma complex processivity proteins and epsilon proofreading exonuclease on nucleotide misincorporation efficiencies

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3325112

Side chains that influence fidelity at the polymerase active site of Escherichia coli DNA polymerase I (Klenow fragment)

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20152155

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Simulation of conformational transitions by the restricted perturbation-targeted molecular dynamics method

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/20152155

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Constant pressure molecular dynamics simulation: The Langevin piston method

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2009.10.014

Comparison of simple potential functions for simulating liquid water

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2009.10.014

A smooth particle mesh Ewald method

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2009.10.014

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

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2009.10.014

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

1 reference

11 October 2022

https://opencitations.net/index/coci/api/v1/references/10.1016/J.STR.2009.10.014

Identifiers

DOI

10.1016/J.STR.2009.10.014

0 references

Fatcat ID

release_6oox75omdrfzzkfdtlgdrlhgpa

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/6oox75omdrfzzkfdtlgdrlhgpa