(Q42425546)

reason for preferred rank

31 October 2017

Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF) (English)

1 reference

17 July 2024

Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF) (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

17 July 2024

0 references

1 reference

Yue Yang

2

1 reference

31 October 2017

Bing Wang

3

1 reference

31 October 2017

László Füsti-Molnár

4

1 reference

31 October 2017

Martin B. Peters

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

17 July 2024

Michael N. Weaver

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

17 July 2024

Kenneth M. Merz

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

17 July 2024

language of work or name

1 reference

1 September 2010

1 reference

31 October 2017

14 September 2010

1 reference

National Center for Biotechnology Information

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&retmode=json&id=20856692

full work available at URL

17 July 2024

https://europepmc.org/articles/pmc2941202?pdf=render

file format

Portable Document Format

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

https://europepmc.org/articles/PMC2941202

17 July 2024

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

https://europepmc.org/articles/PMC2941202?pdf=render

17 July 2024

file format

Portable Document Format

online access status

open access

content deliverer

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

https://doi.org/10.1021/ct1002626

17 July 2024

online access status

open access

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?resulttype=core&format=json&query=SRC%3AMED%20AND%20EXT_ID%3A20856692

https://pubs.acs.org/doi/pdf/10.1021/ct1002626

17 July 2024

1 reference

Journal of Chemical Theory and Computation

17 July 2024

published in

1 reference

31 October 2017

6

1 reference

31 October 2017

9

1 reference

31 October 2017

2935-2947

1 reference

Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations.

31 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Development, validation, and applications of anisotropic polarizable molecular mechanics to study ligand and drug-receptor interactions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Quantum mechanical and molecular dynamics simulations of ureases and Zn beta-lactamases.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Small revisions to predicted distances around metal sites in proteins

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Geometry of metal-ligand interactions in proteins

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

The geometry of metal-ligand interactions relevant to proteins. II. Angles at the metal atom, additional weak metal-donor interactions.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

The geometry of metal-ligand interactions relevant to proteins.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Protein strain in blue copper proteins studied by free energy perturbations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Molecular dynamics simulations of the resting and hydrogen peroxide-bound states of cytochrome c peroxidase

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

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

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Computational studies of the farnesyltransferase ternary complex part I: substrate binding

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short-range contributions. Comparisons with parallel ab initio computations.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Zn protein simulations including charge transfer and local polarization effects

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

The architecture of metal coordination groups in proteins

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Molecular mechanics force field parameterization of the fluorescent probe rhodamine 6G using automated frequency matching.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Molecular dynamics simulations of the dinuclear zinc-beta-lactamase from Bacteroides fragilis complexed with imipenem

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Insights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

A new molecular mechanics force field for the oxidized form of blue copper proteins

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

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

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

The influence of axial ligands on the reduction potential of blue copper proteins.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

On the role of Glu-68 in alcohol dehydrogenase

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Molecular Dynamics Simulations of the Enzyme Cu, Zn Superoxide Dismutase

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2941202

Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium

1 December 2018

1 reference

12 December 2020

Systematic Derivation of AMBER Force Field Parameters Applicable to Zinc-Containing Systems

1 reference

12 December 2020

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

1 reference

12 December 2020

Modeling enzymatic reactions involving transition metals

1 reference

12 December 2020

Molecular Mechanics (MM3) Parameters for Ruthenium(II)-Polypyridyl Complexes

1 reference

12 December 2020

Empirical force fields for biologically active divalent metal cations in water

1 reference

12 December 2020

A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model

4

1 reference

New Class IV Charge Model for Extracting Accurate Partial Charges from Wave Functions

17 July 2024

5

1 reference

UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations

17 July 2024

15

1 reference

The structure of cobalt corrinoids based on molecular mechanics and NOE-restrained molecular mechanics and dynamics simulations

17 July 2024

21

1 reference

Journal of Inorganic Biochemistry

17 July 2024

45

86

397

Remenyi R.

2001

1 reference

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

17 July 2024

54

1 reference

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

17 July 2024

55

1 reference

van der Waals Volumes and Radii

17 July 2024

62

1 reference

17 July 2024

Identifiers

DOI

10.1021/CT1002626

1 reference

31 October 2017

1 reference

31 October 2017

1 reference