AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins (Q34089389)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24931227 AND SRC:MED&resulttype=core&format=json

20 March 2020

title

AutoDock4(Zn): an improved AutoDock force field for small-molecule docking to zinc metalloproteins (English)

1 reference

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20 March 2020

1 reference

1

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20 March 2020

Maria J. Ramos

series ordinal

3

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20 March 2020

author name string

Stefano Forli

series ordinal

2

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20 March 2020

Arthur J Olson

series ordinal

4

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20 March 2020

publication date

18 July 2014

1 reference

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Journal of Chemical Information and Modeling

20 March 2020

published in

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20 March 2020

volume

54

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20 March 2020

issue

8

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20 March 2020

page(s)

2371-2379

1 reference

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A New Quantum Calibrated Force Field for Zinc-Protein Complex

20 March 2020

cites work

1 reference

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Protein flexibility in virtual screening: the BACE-1 case study

5 July 2018

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Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

5 July 2018

1 reference

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A Force Field with Discrete Displaceable Waters and Desolvation Entropy for Hydrated Ligand Docking

5 July 2018

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A Transferable Non-bonded Pairwise Force Field to Model Zinc Interactions in Metalloproteins

5 July 2018

1 reference

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

5 July 2018

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High-Resolution Crystal Structure of the Subclass B3 Metallo- -Lactamase BJP-1: Rational Basis for Substrate Specificity and Interaction with Sulfonamides

5 July 2018

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AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

5 July 2018

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Modeling of metal interaction geometries for protein-ligand docking.

5 July 2018

1 reference

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A semiempirical free energy force field with charge-based desolvation

5 July 2018

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The design of inhibitors for medicinally relevant metalloproteins

5 July 2018

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Comparison of multiple Amber force fields and development of improved protein backbone parameters

5 July 2018

1 reference

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Comparative evaluation of eight docking tools for docking and virtual screening accuracy

5 July 2018

1 reference

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Crystallographic analysis reveals that anticancer clinical candidate L-778,123 inhibits protein farnesyltransferase and geranylgeranyltransferase-I by different binding modes

5 July 2018

1 reference

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Structural analysis of neprilysin with various specific and potent inhibitors

5 July 2018

1 reference

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Vasopeptidase inhibitors, neutral endopeptidase inhibitors, and dual inhibitors of angiotensin-converting enzyme and neutral endopeptidase

5 July 2018

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Geometry of metal-ligand interactions in proteins

5 July 2018

1 reference

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Zinc finger proteins: new insights into structural and functional diversity

5 July 2018

1 reference

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Python: a programming language for software integration and development

5 July 2018

1 reference

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Carboxylate binding modes in zinc proteins: a theoretical study

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4144784

Recruiting Zn2 to mediate potent, specific inhibition of serine proteases

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4144784

Analysis of zinc binding sites in protein crystal structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4144784

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation

5 July 2018

1 reference

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The structure of a complex between carbonic anhydrase II and a new inhibitor, trifluoromethane sulphonamide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4144784

Zinc coordination, function, and structure of zinc enzymes and other proteins

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4144784

The protein data bank: A computer-based archival file for macromolecular structures

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4144784

Molecular dynamics simulation and molecular docking studies of Angiotensin converting enzyme with inhibitor lisinopril and amyloid Beta Peptide

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4144784

Zinc Chelation with Hydroxamate in Histone Deacetylases Modulated by Water Access to the Linker Binding Channel

28 October 2018

1 reference

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An improved scoring function for suboptimal polar ligand complexes

28 October 2018

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Glutaminyl cyclase inhibition attenuates pyroglutamate Abeta and Alzheimer's disease-like pathology

28 October 2018

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The carboxylate shift in zinc enzymes: a computational study.

28 October 2018

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Zn protein simulations including charge transfer and local polarization effects

28 October 2018

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Ternary ligand-zinc-hydroxamate complexes

28 October 2018

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Modified AutoDock for accurate docking of protein kinase inhibitors

28 October 2018

1 reference

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Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock

28 October 2018

1 reference

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The Zinc proteome: a tale of stability and functionality

28 October 2018

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Analysis of the structural consensus of the zinc coordination centers of metalloprotein structures

28 October 2018

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12 December 2020

Zinc coordination spheres in protein structures

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12 December 2020

Lennard-Jones potential and dummy atom settings to overcome the AUTODOCK limitation in treating flexible ring systems

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12 December 2020

A bioinformatics view of zinc enzymes

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12 December 2020

Docking ligands into flexible and solvated macromolecules. 6. Development and application to the docking of HDACs and other zinc metalloenzymes inhibitors

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12 December 2020

Binding MOAD (Mother Of All Databases)

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12 December 2020

Docking studies of matrix metalloproteinase inhibitors: zinc parameter optimization to improve the binding free energy prediction

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12 December 2020

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

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12 December 2020

CurlySMILES: a chemical language to customize and annotate encodings of molecular and nanodevice structures

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COCI

https://opencitations.net/index/coci/api/v1/citations/10.1186/1758-2946-3-1

Open Babel: An open chemical toolbox

2 January 2022

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25 May 2024

https://opencitations.net/index/api/v1/citations/10.1186/1758-2946-3-33

Identifiers

DOI

10.1021/CI500209E

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24931227 AND SRC:MED&resulttype=core&format=json

journals/jcisd/Santos-MartinsFRO14

20 March 2020

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24931227 AND SRC:MED&resulttype=core&format=json

20 March 2020

PubMed publication ID

24931227

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24931227 AND SRC:MED&resulttype=core&format=json