(Q38032573)

27 August 2017

title

Computational enzymatic catalysis--clarifying enzymatic mechanisms with the help of computers (English)

1 reference

Pedro Alexandrino Fernandes

27 August 2017

Sérgio Filipe Sousa

1

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object named as

Pedro Alexandrino Fernandes

series ordinal

2

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Maria J. Ramos

object named as

Maria João Ramos

series ordinal

3

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language of work or name

English

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publication date

6 August 2012

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Physical Chemistry Chemical Physics

27 August 2017

published in

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27 August 2017

volume

14

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27 August 2017

issue

36

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27 August 2017

page(s)

12431-12441

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Molecular Architecture and Biological Reactions

27 August 2017

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Energetics of enzyme catalysis

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Unified Approach for Molecular Dynamics and Density-Functional Theory

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

21 January 2018

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Reaction mechanism of cis-3-chloroacrylic acid dehalogenase: a theoretical study

21 January 2018

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The reaction mechanism of phenylethanolamine N-methyltransferase: a density functional theory study.

21 January 2018

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Theoretical study of the suicide inhibition mechanism of the enzyme pyruvate formate lyase by methacrylate.

21 January 2018

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Mechanisms of metalloenzymes studied by quantum chemical methods

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Density functional theory of biologically relevant metal centers

21 January 2018

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Reaction mechanism of the binuclear zinc enzyme glyoxalase II - A theoretical study

21 January 2018

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Reaction mechanism of the dinuclear zinc enzyme N-acyl-L-homoserine lactone hydrolase: a quantum chemical study

21 January 2018

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Dipeptide hydrolysis by the dinuclear zinc enzyme human renal dipeptidase: mechanistic insights from DFT calculations

21 January 2018

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Reaction mechanism of the trinuclear zinc enzyme phospholipase C: a density functional theory study

21 January 2018

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Phosphate mono- and diesterase activities of the trinuclear zinc enzyme nuclease P1--insights from quantum chemical calculations.

21 January 2018

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The search for the mechanism of the reaction catalyzed by farnesyltransferase.

21 January 2018

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The carboxylate shift in zinc enzymes: a computational study.

21 January 2018

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Farnesyltransferase--new insights into the zinc-coordination sphere paradigm: evidence for a carboxylate-shift mechanism

21 January 2018

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Determination of the catalytic pathway of a manganese arginase enzyme through density functional investigation

21 January 2018

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Atomistic details of the Catalytic Mechanism of Fe(III)-Zn(II) Purple Acid Phosphatase.

21 January 2018

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Catalytic activity of a ζ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms

21 January 2018

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Density-functional exchange-energy approximation with correct asymptotic behavior

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

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

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

General performance of density functionals

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

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

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

COSMO: a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model.

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

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

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

Transition state stabilization and substrate strain in enzyme catalysis: ab initio QM/MM modelling of the chorismate mutase reaction.

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

Catalytic mechanism and energy barriers for butyrylcholinesterase-catalyzed hydrolysis of cocaine

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

Ab initio QM/MM study of class A beta-lactamase acylation: dual participation of Glu166 and Lys73 in a concerted base promotion of Ser70.

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

Catalytic mechanism and product specificity of the histone lysine methyltransferase SET7/9: an ab initio QM/MM-FE study with multiple initial structures.

21 January 2018

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An all atom force field for simulations of proteins and nucleic acids

21 January 2018

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

21 January 2018

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A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

21 January 2018

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21 January 2018

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All-atom empirical potential for molecular modeling and dynamics studies of proteins

21 January 2018

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Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

21 January 2018

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Development and current status of the CHARMM force field for nucleic acids.

21 January 2018

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The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin

21 January 2018

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Exploring potential energy surfaces for chemical reactions: an overview of some practical methods

21 January 2018

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Born-Oppenheimer ab initio QM/MM molecular dynamics simulations of the hydrolysis reaction catalyzed by protein arginine deiminase 4.

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

Increasing the time step with mass scaling in Born-Oppenheimer ab initio QM/MM molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

cDNA cloning and expression of the peptide-binding β subunit of rat p21rasfarnesyltransferase, the counterpart of yeast DPR1/RAM1

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Cloning and expression of a cDNA encoding the alpha subunit of rat p21ras protein farnesyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Inhibition of purified p21ras farnesyl:protein transferase by Cys-AAX tetrapeptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Protein prenylation: genes, enzymes, targets, and functions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Protein prenylation: molecular mechanisms and functional consequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

All ras proteins are polyisoprenylated but only some are palmitoylated

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Farnesol modification of Kirsten-ras exon 4B protein is essential for transformation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Isoprenoid addition to Ras protein is the critical modification for its membrane association and transforming activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Protein Farnesyltransferase Inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Inhibitors of protein farnesyltransferase as novel anticancer agents

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Farnesyl transferase inhibitors in clinical development

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Development of farnesyl transferase inhibitors: a review

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Lipid posttranslational modifications. Farnesyl transferase inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Farnesyltransferase inhibitors: a detailed chemical view on an elusive biological problem

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Farnesyltransferase inhibitor as anticancer agent

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Protein farnesyltransferase and protein prenylation in Plasmodium falciparum

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Farnesyltransferase inhibitors inhibit the growth of malaria parasites in vitro and in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Structurally simple farnesyltransferase inhibitors arrest the growth of malaria parasites

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Protein farnesyltransferase inhibitors exhibit potent antimalarial activity

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Potent, Plasmodium-selective farnesyltransferase inhibitors that arrest the growth of malaria parasites: structure-activity relationships of ethylenediamine-analogue scaffolds and homology model validation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Development of benzophenone-based farnesyltransferase inhibitors as novel antimalarials

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Cloning, heterologous expression, and distinct substrate specificity of protein farnesyltransferase from Trypanosoma brucei

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Characterization and selective inhibition of myristoyl-CoA:protein N-myristoyltransferase from Trypanosoma brucei and Leishmania major

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Reaction path of protein farnesyltransferase at atomic resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Crystal structure of protein farnesyltransferase at 2.25 angstrom resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Farnesyltransferase inhibitors: promises and realities

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Unraveling the mechanism of the farnesyltransferase enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Detection of farnesyltransferase interface hot spots through computational alanine scanning mutagenesis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Unraveling the Catalytic Pathway of Metalloenzyme Farnesyltransferase through QM/MM Computation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Structural characterization of the zinc site in protein farnesyltransferase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Crystallographic evidence for substrate-assisted catalysis in a bacterial beta-hexosaminidase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Visualizing the reaction coordinate of an O-GlcNAc hydrolase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Development and validation of a genetic algorithm for flexible docking

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Improved protein-ligand docking using GOLD

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

High resolution refinement of β-galactosidase in a new crystal form reveals multiple metal-binding sites and provides a structural basis for α-complementation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Oligosaccharide synthesis by glycosynthases

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Microwave-assisted synthesis of galacto-oligosaccharides from lactose with immobilized beta-galactosidase from Kluyveromyces lactis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

A structural view of the action of Escherichia coli (lacZ) beta-galactosidase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

The structure of E. coli beta-galactosidase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

QM/MM Studies on the β-Galactosidase Catalytic Mechanism: Hydrolysis and Transglycosylation Reactions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Structure-reactivity relationships for beta-galactosidase (Escherichia coli, lac Z). 4. Mechanism for reaction of nucleophiles with the galactosyl-enzyme intermediates of E461G and E461Q beta-galactosidases.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Structure-reactivity relationships for beta-galactosidase (Escherichia coli, lac Z). 3. Evidence that Glu-461 participates in Brønsted acid-base catalysis of beta-D-galactopyranosyl group transfer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Reaction specificity in pyridoxal phosphate enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Molecular mechanisms and therapeutic approaches to the treatment of African trypanosomiasis

21 January 2018

1 reference

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HOMOCYSTINURIA: AN ENZYMATIC DEFECT.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Altering the reaction specificity of eukaryotic ornithine decarboxylase

21 January 2018

1 reference

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Formation of functional cross-species heterodimers of ornithine decarboxylase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Reaction mechanism of caspases: insights from QM/MM Car-Parrinello simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Incorporation of solvent effects into density functional calculations of molecular energies and geometries

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Development and Assessment of a New Hybrid Density Functional Model for Thermochemical Kinetics

21 January 2018

1 reference

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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

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The IEF version of the PCM solvation method: an overview of a new method addressed to study molecular solutes at the QM ab initio level

21 January 2018

1 reference

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Hybrid Models for Combined Quantum Mechanical and Molecular Mechanical Approaches

21 January 2018

1 reference

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Computational Enzymatic Catalysis

21 January 2018

1 reference

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The empirical valence bond model: theory and applications

21 January 2018

1 reference

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Theoretical Study on the Inhibition of Ribonucleotide Reductase by 2‘-Mercapto-2‘-deoxyribonucleoside-5‘-diphosphates

21 January 2018

1 reference

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Enzyme Ribonucleotide Reductase: Unraveling an Enigmatic Paradigm of Enzyme Inhibition by Furanone Derivatives

21 January 2018

1 reference

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In Silico–Based Structural Analysis of Arylthiophene Derivatives for FTase Inhibitory Activity, hERG, and Other Toxic Effects

21 January 2018

1 reference

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Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Farnesyltransferase: Theoretical studies on peptide substrate entrance—thiol or thiolate coordination?

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Theoretical studies on farnesyl transferase: Evidence for thioether product coordination to the active-site zinc sphere

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Theoretical studies on farnesyltransferase: The distances paradox explained

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Effective tailor-made force field parameterization of the several Zn coordination environments in the puzzling FTase enzyme: opening the door to the full understanding of its elusive catalytic mechanism

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Molecular dynamics analysis of farnesyltransferase: A closer look into the amino acid behavior

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human β-HexosaminidaseA

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Theoretical insights into the catalytic mechanism of β-hexosaminidase

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Mechanism of Formation of the Internal Aldimine in Pyridoxal 5′-Phosphate-Dependent Enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1039%2FC2CP41180F

Computational evidence for the substrate-assisted catalytic mechanism of O-GlcNAcase. A DFT investigation

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

Nature of Forces between Large Molecules of Biological Interest*

21 January 2018

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https://api.crossref.org/works/10.1039%2FC2CP41180F

21 January 2018

Identifiers

DOI

10.1039/C2CP41180F

1 reference

27 August 2017

1 reference