(Q28543572)

English

Molecular dynamics of CYP2D6 polymorphisms in the absence and presence of a mechanism-based inactivator reveals changes in local flexibility and dominant substrate access channels

scientific article

In more languages

default for all languages

No label defined

No description defined

Statements

scholarly article

0 references

Molecular dynamics of CYP2D6 polymorphisms in the absence and presence of a mechanism-based inactivator reveals changes in local flexibility and dominant substrate access channels (English)

0 references

molecular dynamics simulation

0 references

1

object named as

Parker W de Waal

author given names

Parker W

author last names

de Waal

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

Laura Lowe Furge

3

object named as

Laura Lowe Furge

author given names

Laura Lowe

author last names

Furge

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

author name string

Kyle F Sunden

2

author given names

Kyle F

author last names

Sunden

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

language of work or name

0 references

publication date

2014

0 references

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

9

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

10

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

e108607

1 reference

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

copyright license

Creative Commons Attribution 4.0 International

6 October 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

0 references

Distal effect of amino acid substitutions in CYP2C9 polymorphic variants causes differences in interatomic interactions against (S)-warfarin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

Structural diversity of eukaryotic membrane cytochrome p450s

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

Potent Mechanism-Based Inactivation of Cytochrome P450 2B4 by 9-Ethynylphenanthrene: Implications for Allosteric Modulation of Cytochrome P450 Catalysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

Crystal Structure of Human Cytochrome P450 2D6 with Prinomastat Bound

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

Crystal structure of human cytochrome P450 2D6

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

The Amber biomolecular simulation programs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

UCSF Chimera--a visualization system for exploratory research and analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

19 March 2017

PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

7 April 2017

Very fast empirical prediction and rationalization of protein pKa values

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

7 April 2017

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

The role of cytochrome P450 2B6 and 2B4 substrate access channel residues predicted based on crystal structures of the amlodipine complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Molecular dynamic investigations of the mutational effects on structural characteristics and tunnel geometry in CYP17A1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Conformational diversity and ligand tunnels of mammalian cytochrome P450s

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Molecular analysis and modeling of inactivation of human CYP2D6 by four mechanism based inactivators.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Is there a relationship between the substrate preferences and structural flexibility of cytochromes P450?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Comparison of cytochrome P450 2D6 and variants in terms of drug oxidation rates and substrate inhibition.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Substituted imidazole of 5-fluoro-2-[4-[(2-phenyl-1H-imidazol-5-yl)methyl]-1-piperazinyl]pyrimidine Inactivates cytochrome P450 2D6 by protein adduction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Anandamide oxidation by wild-type and polymorphically expressed CYP2B6 and CYP2D6.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Prediction and analysis of the modular structure of cytochrome P450 monooxygenases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Two-dimensional NMR and all-atom molecular dynamics of cytochrome P450 CYP119 reveal hidden conformational substates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Polymorphism of human cytochrome P450 2D6 and its clinical significance: Part I.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

New insights into the structural characteristics and functional relevance of the human cytochrome P450 2D6 enzyme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Impact of plasticity and flexibility on docking results for cytochrome P450 2D6: a combined approach of molecular dynamics and ligand docking.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Mechanism-based inactivation of human cytochromes p450s: experimental characterization, reactive intermediates, and clinical implications

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Insights into drug metabolism by cytochromes P450 from modelling studies of CYP2D6-drug interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Molecular insight into the interaction between IFABP and PA by using MM-PBSA and alanine scanning methods

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Structural basis for ligand promiscuity in cytochrome P450 3A4.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

The ins and outs of cytochrome P450s.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Predicting in vivo drug interactions from in vitro drug discovery data

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Genetic polymorphisms of cytochrome P450 2D6 (CYP2D6): clinical consequences, evolutionary aspects and functional diversity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Cytochromes P450, drugs, and diseases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

Polymorphism of the cytochrome P450 CYP2D6 gene in a European population: characterization of 48 mutations and 53 alleles, their frequencies and evolution.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

29 September 2017

CYP 2D6 binding affinity predictions using multiple ligand and protein conformations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

3 June 2018

Structure of microsomal cytochrome P450 2B4 complexed with the antifungal drug bifonazole: insight into P450 conformational plasticity and membrane interaction.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

3 June 2018

Expression, purification, biochemical characterization, and comparative function of human cytochrome P450 2D6.1, 2D6.2, 2D6.10, and 2D6.17 allelic isoforms

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

3 June 2018

Functional characterization of 17 CYP2D6 allelic variants (CYP2D6.2, 10, 14A-B, 18, 27, 36, 39, 47-51, 53-55, and 57).

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

Polymorphism of human cytochrome P450 2D6 and its clinical significance: part II.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

The star-allele nomenclature: retooling for translational genomics

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

Mechanism of the decrease in catalytic activity of human cytochrome P450 2C9 polymorphic variants investigated by computational analysis.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

How well does Poisson-Boltzmann implicit solvent agree with explicit solvent? A quantitative analysis

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

In silico study on the inhibitory interaction of drugs with wild-type CYP2D6.1 and the natural variant CYP2D6.17.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

Flexibility of human cytochromes P450: molecular dynamics reveals differences between CYPs 3A4, 2C9, and 2A6, which correlate with their substrate preferences

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

Identification of a meander region proline residue critical for heme binding to cytochrome P450: implications for the catalytic function of human CYP4B1.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P450 Probed by Molecular Dynamics Simulations

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

Binding of quinidine radically increases the stability and decreases the flexibility of the cytochrome P450 2D6 active site

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108607

21 January 2018

A combination of mutations in the CYP2D6*17 (CYP2D6Z) allele causes alterations in enzyme function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4186923

27 November 2018

Mutation-induced loop opening and energetics for binding of tamiflu to influenza N8 neuraminidase

1 reference

https://pubmed.ncbi.nlm.nih.gov/25286176

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Long-range effects of a peripheral mutation on the enzymatic activity of cytochrome P450 1A2

1 reference

https://pubmed.ncbi.nlm.nih.gov/25286176

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PONE.0108607

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

2014PLoSO...9j8607D

0 references

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

PMC publication ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

PubMed publication ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

Europe PubMed Central

PMC publication ID

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25286176%20AND%20SRC:MED&resulttype=core&format=json

4 June 2020

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

Wiktionary(0 entries)

Multilingual sites(0 entries)

Retrieved from "https://www.wikidata.org/w/index.php?title=Q28543572&oldid=1995268318"