Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle (Q31035806)

15 September 2017

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

1 reference

15 September 2017

Thomas E. Cheatham, III

series ordinal

4

object named as

Thomas E Cheatham

1 reference

15 September 2017

3

Garold S Yost

1 reference

15 September 2017

Kiumars Shahrokh

1

1 reference

PMCID

3242737

15 September 2017

Anita Orendt

series ordinal

2

1 reference

15 September 2017

14 October 2011

1 reference

Journal of Computational Chemistry

15 September 2017

1 reference

15 September 2017

33

1 reference

15 September 2017

2

1 reference

15 September 2017

119-133

1 reference

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

15 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Improved cytochrome P450 3A4 molecular models accurately predict the Phe215 requirement for raloxifene dehydrogenation selectivity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Improved side-chain torsion potentials for the Amber ff99SB protein force field

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

CYP3A4-Mediated oxygenation versus dehydrogenation of raloxifene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Structure-based drug metabolism predictions for drug design.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Discovery through the computational microscope

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Hydrocarbon hydroxylation by cytochrome P450 enzymes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

S K-edge XAS and DFT calculations on cytochrome P450: covalent and ionic contributions to the cysteine-Fe bond and their contribution to reactivity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Cytochrome p450 and chemical toxicology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

State-of-the-art tools for computational site of metabolism predictions: comparative analysis, mechanistical insights, and future applications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Modeling heme proteins using atomistic simulations

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

What common structural features and variations of mammalian P450s are known to date?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Structural basis for ligand promiscuity in cytochrome P450 3A4.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Biomolecular modeling: Goals, problems, perspectives

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

The status of high-valent metal oxo complexes in the P450 cytochromes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Crystal structure of human cytochrome P450 2D6

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

The Amber biomolecular simulation programs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Theoretical perspective on the structure and mechanism of cytochrome P450 enzymes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Structures of cytochrome P450 3A4.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Mechanism of oxidation reactions catalyzed by cytochrome p450 enzymes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Crystal structures of human cytochrome P450 3A4 bound to metyrapone and progesterone

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Development and testing of a general amber force field

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Structure of mammalian cytochrome P450 2B4 complexed with 4-(4-chlorophenyl)imidazole at 1.9-A resolution: insight into the range of P450 conformations and the coordination of redox partner binding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

An open conformation of mammalian cytochrome P450 2B4 at 1.6-Å resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Substrate routes to the buried active site may vary among cytochromes P450: mutagenesis of the F-G region in P450 2B1.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

All-Atom Structure Prediction and Folding Simulations of a Stable Protein

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

The catalytic pathway of cytochrome p450cam at atomic resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3242737

Combined three-dimensional quantitative structure-activity relationship analysis of cytochrome P450 2B6 substrates and protein homology modeling

21 June 2018

1 reference

In silico approaches to predicting drug metabolism, toxicology and beyond.

21 January 2018

1 reference

A truncation of 2B subfamily cytochromes P450 yields increased expression levels, increased solubility, and decreased aggregation while retaining function

21 January 2018

1 reference

Aromatic hydroxylation by cytochrome P450: model calculations of mechanism and substituent effects.

21 January 2018

1 reference

Classical force field parameters for the heme prosthetic group of cytochrome c.

21 January 2018

1 reference

New AMBER force field parameters of heme iron for cytochrome P450s determined by quantum chemical calculations of simplified models.

21 January 2018

1 reference

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

21 January 2018

1 reference

Self‐consistent molecular orbital methods. XXIII. A polarization‐type basis set for second‐row elements

21 January 2018

1 reference

Multireference ab initio quantum mechanics/molecular mechanics study on intermediates in the catalytic cycle of cytochrome P450(cam).

21 January 2018

1 reference

The structure of human microsomal cytochrome P450 3A4 determined by X-ray crystallography to 2.05-A resolution

21 January 2018

1 reference

Validation of Exchange−Correlation Functionals for Spin States of Iron Complexes

21 January 2018

1 reference

Parametrized Models of Aqueous Free Energies of Solvation Based on Pairwise Descreening of Solute Atomic Charges from a Dielectric Medium

21 January 2018

1 reference

Comparison of simple potential functions for simulating liquid water

21 January 2018

1 reference

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

21 January 2018

1 reference

Density-functional thermochemistry. III. The role of exact exchange

21 January 2018

1 reference

Accurate spin-dependent electron liquid correlation energies for local spin density calculations: a critical analysis

21 January 2018

1 reference

Hydroxylation of camphor by reduced oxy-cytochrome P450cam: mechanistic implications of EPR and ENDOR studies of catalytic intermediates in native and mutant enzymes

21 January 2018

1 reference

Quantum mechanical/molecular mechanical investigation of the mechanism of C-H hydroxylation of camphor by cytochrome P450cam: theory supports a two-state rebound mechanism

21 January 2018

1 reference

Dynamic simulations of oxygen binding to myoglobin

21 January 2018

1 reference

12 December 2020

General Transition-State Force Field for Cytochrome P450 Hydroxylation

1 reference

12 December 2020

Calculation of the electronic structure and spectra of model cytochrome P450 compound I

1 reference

12 December 2020

Peculiarities of the Electronic Structure of Cytochrome P450 Compound I: CASPT2 and DFT Modeling

1 reference

12 December 2020

Molecular modeling of cytochrome P450 3A4

1 reference

12 December 2020

Identifiers

DOI

10.1002/JCC.21922

1 reference

journals/jcc/ShahrokhOYC12

15 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

15 September 2017

1 reference

PMCID

3242737