(Q26823476)

molecular dynamics simulation

main subject

1 reference

19 September 2019

1 reference

1 May 2021

1 reference

PubMed publication ID

25006697

quantum mechanics

1 reference

PubMed publication ID

25006697

author

Alessandra Magistrato

series ordinal

2

object named as

Alessandra Magistrato

1 reference

1

Pietro Vidossich

1 reference

language of work or name

1 reference

8 July 2014

5 references

19 September 2019

4 November 2019

1 May 2021

28 October 2023

5 references

19 September 2019

4 November 2019

1 May 2021

28 October 2023

4

1 reference

issue

3

1 reference

page(s)

616-45

1 reference

Creative Commons Attribution

copyright license

4 references

19 September 2019

4 November 2019

1 May 2021

28 October 2023

0 references

The origins of the RNA world

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

MeRNA: a database of metal ion binding sites in RNA structures

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Generalized Gradient Approximation Made Simple

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Unified Approach for Molecular Dynamics and Density-Functional Theory

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

The structural basis of RNA-catalyzed RNA polymerization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Catalase-peroxidase KatG of Burkholderia pseudomallei at 1.7A resolution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Effect of arginine-48 replacement on the reaction between cytochrome c peroxidase and hydrogen peroxide

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Histidine 52 is a critical residue for rapid formation of cytochrome c peroxidase compound I

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Three-dimensional structure of catalase from Penicillium vitale at 2.0 A resolution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Alpha-synuclein in Lewy bodies

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Alpha-synuclein and neurodegenerative diseases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Critical role of magnesium ions in DNA polymerase beta's closing and active site assembly

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Diversity of structures and properties among catalases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Density-functional exchange-energy approximation with correct asymptotic behavior

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the post-hydrolysis reactions

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

A mechanism for all 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=4192665

Structural Determinants of Cisplatin and Transplatin Binding to the Met-Rich Motif of Ctr1: A Computational Spectroscopy Approach

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Perspective: Fifty years of density-functional theory in chemical physics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Calcium inhibition of ribonuclease H1 two-metal ion catalysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Electron flow in multiheme bacterial cytochromes is a balancing act between heme electronic interaction and redox potentials

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

In-ice evolution of RNA polymerase ribozyme activity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

The S2 state of the oxygen-evolving complex of photosystem II explored by QM/MM dynamics: spin surfaces and metastable states suggest a reaction path towards the S3 state

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Designing functional metalloproteins: from structural to catalytic metal sites

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Antibiotic resistance in Zn(II)-deficient environments: metallo-β-lactamase activation in the periplasm.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Biapenem inactivation by B2 metallo β-lactamases: energy landscape of the hydrolysis reaction

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

First-principles modeling of biological systems and structure-based drug-design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Specific function of the Met-Tyr-Trp adduct radical and residues Arg-418 and Asp-137 in the atypical catalase reaction of catalase-peroxidase KatG

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Cations in charge: magnesium ions in RNA folding and catalysis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Biomolecular simulation: a computational microscope for molecular biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Challenges for density functional theory.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Ribozyme-catalyzed transcription of an active ribozyme

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Structures behind the amyloid aggregation of α-synuclein: an NMR based approach

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Bridging quantum mechanics and structure-based drug design

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

QM/MM studies of monozinc β-lactamase CphA suggest that the crystal structure of an enzyme-intermediate complex represents a minor pathway.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Metalloproteomics: forward and reverse approaches in metalloprotein structural and functional characterization

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

A self-learning algorithm for biased molecular dynamics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Metals, oxidative stress and neurodegenerative disorders

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Mechanisms of catalase activity of heme peroxidases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Thirty years of heme peroxidase structural biology

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

C-H bond activation in transition metal species from a computational perspective

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Density functional theory for transition metals and transition metal chemistry

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

A molecular dynamics study of the hydroxyl radical in solution applying self-interaction-corrected density functional methods.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Metalloproteomes: a bioinformatic approach.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Common mechanistic features among metallo-beta-lactamases: a computational study of Aeromonas hydrophila CphA enzyme

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

QM/MM methods for biomolecular systems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle DFsc peptides: implications for O2 reactivity of binuclear non-heme iron enzymes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

DNA structural distortions induced by ruthenium-arene anticancer compounds.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

28 September 2017

The Janus nature of heme

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Investigating biological systems using first principles Car-Parrinello molecular dynamics simulations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Role of zinc content on the catalytic efficiency of B1 metallo beta-lactamases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas aeruginosa.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Magnesium-cationic dummy atom molecules enhance representation of DNA polymerase beta in molecular dynamics simulations: improved accuracy in studies of structural features and mutational effects

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Metallo-beta-lactamases: novel weaponry for antibiotic resistance in bacteria

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Probing the structure and bifunctionality of catalase-peroxidase (KatG).

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Replica exchange with solute tempering: a method for sampling biological systems in explicit water

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Structural characterization of copper(II) binding to alpha-synuclein: Insights into the bioinorganic chemistry of Parkinson's disease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Release of long-range tertiary interactions potentiates aggregation of natively unstructured alpha-synuclein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Time-dependent density functional theory.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

28 September 2017

Heme protein assemblies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Oxidizing enzymes as biocatalysts.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Escaping free-energy minima

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

The role and perspective of ab initio molecular dynamics in the study of biological systems

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Construction of heme enzymes: four approaches

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

28 September 2017

Non-heme iron oxygenases

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Redox metals and neurodegenerative disease

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Density-functional approximation for the correlation energy of the inhomogeneous electron gas

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Iron-sulfur clusters: nature's modular, multipurpose structures

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Beta-lactamases and bacterial resistance to antibiotics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Iron transport and storage proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Identification by ENDOR of Trp191 as the free-radical site in cytochrome c peroxidase compound ES.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Enzyme immunoassay techniques an overview

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Exploring the structural details of Cu(I) binding to α-synuclein by NMR spectroscopy

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

A molecular switch and electronic circuit modulate catalase activity in catalase-peroxidases

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4192665

A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations

31 May 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Binding of novel azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid QM/MM molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

The hydrolysis mechanism of the anticancer ruthenium drugs NAMI-A and ICR investigated by DFT-PCM calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Copper-1,10-phenanthroline complexes binding to DNA: structural predictions from molecular simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Automated Parametrization of AMBER Force Field Terms from Vibrational Analysis with a Focus on Functionalizing Dinuclear Zinc(II) Scaffolds.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Systematic first principles parameterization of force fields for metal-organic frameworks using a genetic algorithm approach

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Computational perspective on Pd-catalyzed C-C cross-coupling reaction mechanisms.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Inhomogeneous Electron Gas

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Self-Consistent Equations Including Exchange and Correlation Effects

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other fun

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Semiempirical GGA-type density functional constructed with a long-range dispersion correction.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Calculation of redox properties: understanding short- and long-range effects in rubredoxin

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

An Efficient Real Space Multigrid QM/MM Electrostatic Coupling.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

An Efficient Linear-Scaling Electrostatic Coupling for Treating Periodic Boundary Conditions in QM/MM Simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Frontier Bonds in QM/MM Methods: A Comparison of Different Approaches

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

The molecular mechanism of the catalase reaction

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Two [Fe(IV)=O Trp*] intermediates in M. tuberculosis catalase-peroxidase discriminated by multifrequency (9-285 GHz) EPR spectroscopy: reactivity toward isoniazid

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

On the active site of mononuclear B1 metallo β-lactamases: a computational study

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Water-assisted reaction mechanism of monozinc beta-lactamases

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

A quantum mechanics/molecular mechanics study on the hydrolysis mechanism of New Delhi metallo-β-lactamase-1.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

A metallo-beta-lactamase enzyme in action: crystal structures of the monozinc carbapenemase CphA and its complex with biapenem

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

A bioinorganic view of Alzheimer's disease: when misplaced metal ions (re)direct the electrons to the wrong target

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Bioinorganic Chemistry of Parkinson’s Disease: Structural Determinants for the Copper-Mediated Amyloid Formation of Alpha-Synuclein

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Double-Metal-Ion/Single-Metal-Ion Mechanisms of the Cleavage Reaction of Ribozymes: First-Principles Molecular Dynamics Simulations of a Fully Hydrated Model System.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Accelerated molecular dynamics: a promising and efficient simulation method for biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Automated Parametrization of Biomolecular Force Fields from Quantum Mechanics/Molecular Mechanics (QM/MM) Simulations through Force Matching.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Optical spectra of Cu(II)-azurin by hybrid TDDFT-molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Free energies for biological electron transfer from QM/MM calculation: method, application and critical assessment.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Extension of QM/MM docking and its applications to metalloproteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Prediction of molecular properties and molecular spectroscopy with density functional theory: From fundamental theory to exchange-coupling

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

A critical evaluation of DFT, including time-dependent DFT, applied to bioinorganic chemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

The Effect of a Water Molecule on the Mechanism of Formation of Compound 0 in Horseradish Peroxidase

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Mapping Long-Range Interactions in α-Synuclein using Spin-Label NMR and Ensemble Molecular Dynamics Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Parameterization of azole-bridged dinuclear platinum anticancer drugs via a QM/MM force matching procedure

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

A Variational Definition of Electrostatic Potential Derived Charges

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Bioinorganic chemistry of copper coordination to alpha-synuclein: Relevance to Parkinson's disease

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

Azole-bridged diplatinum anticancer compounds. Modulating DNA flexibility to escape repair mechanism and avoid cross resistance

21 January 2018

1 reference

12 December 2020

Structure and Raman spectrum of clavulanic acid in aqueous solution

1 reference

12 December 2020

The active center of catalase

1 reference

12 December 2020

Reactivity of horseradish peroxidase compound II toward substrates: kinetic evidence for a two-step mechanism

1 reference

12 December 2020

Quantum Mechanical and Quantum Mechanical/Molecular Mechanical Studies of the Iron-Dioxygen Intermediates and Proton Transfer in Superoxide Reductase

1 reference

12 December 2020

The structural role of Mg2+ ions in a class I RNA polymerase ribozyme: a molecular simulation study

1 reference

12 December 2020

Elementary steps in the formation of horseradish peroxidase compound I: direct observation of compound 0, a new intermediate with a hyperporphyrin spectrum

1 reference

12 December 2020

Simulation of heme using DFT + U: a step toward accurate spin-state energetics

1 reference

12 December 2020

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

1 reference

12 December 2020

Computational transition metal chemistry

1 reference

12 December 2020

Metabolism of hydrogen peroxide in isolated hepatocytes: Relative contributions of catalase and glutathione peroxidase in decomposition of endogenously generated H2O2

1 reference

12 December 2020

Detecting DNA mismatches with metallo-insertors: a molecular simulation study

1 reference

12 December 2020

On the mechanism of compound I formation from peroxidases and catalases

1 reference

12 December 2020

Protonation state and substrate binding to B2 metallo-beta-lactamase CphA from Aeromonas hydrofila

1 reference

12 December 2020

Versatility of the Electronic Structure of Compound I in Catalase-Peroxidases

1 reference

12 December 2020

The stereochemistry of peroxidase catalysis

1 reference

12 December 2020

Catalases versus peroxidases: DFT investigation of H2O2 oxidation in models systems and implications for heme protein engineering

1 reference

12 December 2020

The description of electronic processes inside proteins from Car-Parrinello molecular dynamics: chemical transformations

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

7 January 2021

inferred from DOI database lookup

Zinc Metallo-β-Lactamase fromBacteroides fragilis: A Quantum Chemical Study on Model Systems of the Active Site

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

7 January 2021

inferred from DOI database lookup

Oxygen Binding to Catalase-Peroxidase

1 reference

https://api.crossref.org/works/10.3390%2FBIOM4030616

7 January 2021

inferred from DOI database lookup

Identifiers

0 references

1 reference

PubMed publication ID

25006697

1 reference