In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function (Q58042970)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

5 May 2020

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

5 May 2020

Katie Mitchell-Koch

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

5 May 2020

publication date

14 July 2017

0 references

published in

Catalysts

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

5 May 2020

volume

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

5 May 2020

page(s)

212

0 references

issue

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

5 May 2020

copyright license

start time

14 July 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Conformational Sub-states and Populations in Enzyme Catalysis

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein conformational populations and functionally relevant substates.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Computational approaches: reaction trajectories, structures, and atomic motions. Enzyme reactions and proficiency

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Electrostatic basis for enzyme catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Global dynamics of proteins: bridging between structure and function

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Force spectroscopy studies on protein-ligand interactions: a single protein mechanics perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Recent advances in FRET for the study of protein interactions and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of dynamics in enzyme catalysis: substantial versus semantic controversies

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The dynamical nature of enzymatic catalysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Einfluss der Configuration auf die Wirkung der Enzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Application of a Theory of Enzyme Specificity to Protein Synthesis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conformational selection in protein binding and function

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Essential role of conformational selection in ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Enzymatic transition states and dynamic motion in barrier crossing

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Insights into Protein-Ligand Interactions: Mechanisms, Models, and Methods

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conformational selection and induced fit mechanism underlie specificity in noncovalent interactions with ubiquitin

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

A role for both conformational selection and induced fit in ligand binding by the LAO protein

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Intrinsic dynamics of an enzyme underlies catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of Conformational Motions in Enzyme Function: Selected Methodologies and Case Studies.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Keep on moving: discovering and perturbing the conformational dynamics of enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Perspective: Defining and quantifying the role of dynamics in enzyme catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conformational change in substrate binding, catalysis and product release: an open and shut case?

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Enzymes: An integrated view of structure, dynamics and function

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

A hierarchy of timescales in protein dynamics is linked to enzyme catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Diffraction, crystallography and microscopy beyond three dimensions: structural dynamics in space and time

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Using NMR spectroscopy to elucidate the role of molecular motions in enzyme function

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

A practical guide to modelling enzyme-catalysed reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Multi-scale computational enzymology: enhancing our understanding of enzymatic catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Biomolecular simulation: a computational microscope for molecular biology

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Current state-of-the-art molecular dynamics methods and applications.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein dynamics and function: insights from the energy landscape and solvent slaving

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Slaving: solvent fluctuations dominate protein dynamics and functions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Coupling of protein and hydration-water dynamics in biological membranes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Reconciling mediating and slaving roles of water in protein conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Binding of small-molecule ligands to proteins: "what you see" is not always "what you get".

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Free-Energy Landscape of Protein-Ligand Interactions Coupled with Protein Structural Changes.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Entropy is key to the formation of pentacyclic terpenoids by enzyme-catalyzed polycyclization

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water-Restructuring Mutations Can Reverse the Thermodynamic Signature of Ligand Binding to Human Carbonic Anhydrase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Redesign of water networks for efficient biocatalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Exploring water as building bricks in enzyme engineering.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Long-timescale molecular dynamics simulations of protein structure and function.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Reaching biological timescales with all-atom molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Molecular dynamics simulations of large macromolecular complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Crystal structure of E.coli alcohol dehydrogenase YqhD: evidence of a covalently modified NADP coenzyme

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water as an active constituent in cell biology

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water mediation in protein folding and molecular recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

From protein folding to protein function and biomolecular binding by energy landscape theory

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Biomolecular hydration dynamics: a jump model perspective

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water structure and interactions with protein surfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The Multiple Roles of Waters in Protein Solvation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The role of conserved waters in conformational transitions of Q61H K-ras

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamics of water in biological recognition

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Hydration in protein crystallography

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein hydration in solution: experimental observation by x-ray and neutron scattering

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Description of Hydration Water in Protein (Green Fluorescent Protein) Solution.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water hydrogen bond analysis on hydrophilic and hydrophobic biomolecule sites

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Hydration-coupled dynamics in proteins studied by neutron scattering and NMR: the case of the typical EF-hand calcium-binding parvalbumin

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Applications of 2D IR spectroscopy to peptides, proteins, and hydrogen-bond dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Small-angle scattering: a view on the properties, structures and structural changes of biological macromolecules in solution

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Applications of small-angle X-ray scattering to biomacromolecular solutions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Identifying and Visualizing Macromolecular Flexibility in Structural Biology

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water Dynamics in the Hydration Shells of Biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamics of folded proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The role of conserved water molecules in the catalytic domain of protein kinases

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Structural basis of human triosephosphate isomerase deficiency: mutation E104D is related to alterations of a conserved water network at the dimer interface

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Site-specific hydration dynamics in the nonpolar core of a molten globule by dynamic nuclear polarization of water

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein hydration dynamics in solution: a critical survey

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Analysis of protein conformation and dynamics by hydrogen/deuterium exchange MS.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein Footprinting Comes of Age: Mass Spectrometry for Biophysical Structure Assessment

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Mass spectrometry: come of age for structural and dynamical biology.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Mass Spectrometry: A Technique of Many Faces

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The Evolving Contribution of Mass Spectrometry to Integrative Structural Biology

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Hydrogen exchange mass spectrometry for studying protein structure and dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Future directions of structural mass spectrometry using hydroxyl radical footprinting

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Residence times of water molecules in the hydration sites of myoglobin

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Mapping hydration dynamics around a protein surface

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Biomolecular hydration: From water dynamics to hydrodynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Comparative study of hydration shell dynamics around a hyperactive antifreeze protein and around ubiquitin.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Analysis of factors influencing hydration site prediction based on molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The role of water molecules in computational drug design

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The Roles of Water in the Protein Matrix: A Largely Untapped Resource for Drug Discovery.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of the active-site solvent in the thermodynamics of factor Xa ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

WATsite: hydration site prediction program with PyMOL interface

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The lubricant of life: a proposal that solvent water promotes extremely fast conformational fluctuations in mobile heteropolypeptide structure

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

A molecular jump mechanism of water reorientation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

First and Second One-Electron Reduction of Lumiflavin in Water-A First Principles Molecular Dynamics Study

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

H and other transfers in enzymes and in solution: theory and computations, a unified view. 2. Applications to experiment and computations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Hydrogen tunneling and protein motion in enzyme reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Theory of proton-coupled electron transfer in energy conversion processes

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The terahertz dance of water with the proteins: the effect of protein flexibility on the dynamical hydration shell of ubiquitin

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamics and mechanism of ultrafast water-protein interactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Adhesive water networks facilitate binding of protein interfaces

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamics at the protein-water interface from 17O spin relaxation in deeply supercooled solutions.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The Dynamics of Water−Protein Interaction Studied by Ultrafast Optical Kerr-Effect Spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Ultrafast dynamics and hydrogen-bond structure in aqueous solutions of model peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

An extended dynamical hydration shell around proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Enzymatic turnover of macromolecules generates long-lasting protein-water-coupled motions beyond reaction steady state

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Surface water retardation around single-chain polymeric nanoparticles: critical for catalytic function?

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamics of biological macromolecules: not a simple slaving by hydration water.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of Internal Water on Protein Thermal Stability: The Case of Homologous G Domains

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Classification of water molecules in protein binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Rapid and accurate prediction and scoring of water molecules in protein binding sites

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

WaterScore: a novel method for distinguishing between bound and displaceable water molecules in the crystal structure of the binding site of protein-ligand complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

PyWATER: a PyMOL plug-in to find conserved water molecules in proteins by clustering.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conserved water molecules in MHC class-I molecules and their putative structural and functional roles.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Stabilizing of a globular protein by a highly complex water network: a molecular dynamics simulation study on factor Xa.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conserved water molecules in family 1 glycosidases: a DXMS and molecular dynamics study.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Computer simulations study of biomolecules in non-aqueous or cosolvent/water mixture solutions.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Hydration of enzyme in nonaqueous media is consistent with solvent dependence of its activity

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

To Keep or Not to Keep? The Question of Crystallographic Waters for Enzyme Simulations in Organic Solvent.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Effects of organic solvents and substrate binding on trypsin in acetonitrile and hexane media

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Locating and characterizing binding sites on proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Multiple solvent crystal structures: probing binding sites, plasticity and hydration

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Driving Structure-Based Drug Discovery through Cosolvent Molecular Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Advances in time-resolved approaches to characterize the dynamical nature of enzymatic catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conformational plasticity of an enzyme during catalysis: intricate coupling between cyclophilin A dynamics and substrate turnover

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of protein dynamics in reaction rate enhancement by enzymes.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

A link between protein structure and enzyme catalyzed hydrogen tunneling

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Combined quantum mechanics/molecular mechanics (QM/MM) methods in computational enzymology

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

QM/MM free energy simulations: recent progress and challenges

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of substrate dynamics in protein prenylation reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Crystal structure of farnesyl protein transferase complexed with a CaaX peptide and farnesyl diphosphate analogue

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Substrate tunnels in enzymes: structure-function relationships and computational methodology

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein Binding Pocket Dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Tunneling of intermediates in enzyme-catalyzed reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Ligand diffusion in proteins via enhanced sampling in molecular dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Does metabolite channeling accelerate enzyme-catalyzed cascade reactions?

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Roles of Asp75, Asp78, and Glu83 of GTP-dependent phosphoenolpyruvate carboxykinase from Mycobacterium smegmatis.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Electrostatic interactions play a significant role in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn2+.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Site-directed mutagenesis study of the microenvironment characteristics of Lys213 of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Relevance of phenylalanine 216 in the affinity of Saccharomyces cerevisiae phosphoenolpyruvate carboxykinase for Mn(II).

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Uncovering a dynamically formed substrate access tunnel in carbon monoxide dehydrogenase/acetyl-CoA synthase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

A combined theoretical and experimental study of the ammonia tunnel in carbamoyl phosphate synthetase

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Mechanism for the transport of ammonia within carbamoyl phosphate synthetase determined by molecular dynamics simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Carbamate transport in carbamoyl phosphate synthetase: a theoretical and experimental investigation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The molecular basis of substrate channeling

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Evidence for hysteretic substrate channeling in the proline dehydrogenase and Δ1-pyrroline-5-carboxylate dehydrogenase coupled reaction of proline utilization A (PutA).

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Binding and channeling of alternative substrates in the enzyme DmpFG: a molecular dynamics study.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

From structure to catalysis: recent developments in the biotechnological applications of lipases

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Solvent-induced lid opening in lipases: a molecular dynamics study

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Unlocking the mystery behind the activation phenomenon of T1 lipase: a molecular dynamics simulations approach

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Statistically optimal analysis of samples from multiple equilibrium states

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Specific Inter-residue Interactions as Determinants of Human Monoacylglycerol Lipase Catalytic Competency: A ROLE FOR GLOBAL CONFORMATIONAL CHANGES.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Structural and dynamic properties of cytochrome P450 BM-3 in pure water and in a dimethylsulfoxide/water mixture

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Toward understanding the inactivation mechanism of monooxygenase P450 BM-3 by organic cosolvents: a molecular dynamics simulation study.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Understanding a mechanism of organic cosolvent inactivation in heme monooxygenase P450 BM-3

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of protein motions on proton transfer pathways in human carbonic anhydrase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Structural and Kinetic Study of the Extended Active Site for Proton Transfer in Human Carbonic Anhydrase II

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Determination of the Reaction Coordinate for a Key Conformational Fluctuation in Human Carbonic Anhydrase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Transition path sampling study of the conformational fluctuation of His-64 in human carbonic anhydrase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Elucidation of the proton transport mechanism in human carbonic anhydrase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Coupling Protein Dynamics with Proton Transport in Human Carbonic Anhydrase II.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein electron transfer rates set by the bridging secondary and tertiary structure

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Laboratory evolution of P450 BM3 for mediated electron transfer yielding an activity-improved and reductase-independent variant

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Insight into the redox partner interaction mechanism in cytochrome P450BM-3 using molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Equilibrium and transient state spectrophotometric studies of the mechanism of reduction of the flavoprotein domain of P450BM-3.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Steering electrons on moving pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Electron transfer, decoherence, and protein dynamics: insights from atomistic simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conformational Dynamics of the FMN-Binding Reductase Domain of Monooxygenase P450BM-3.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

MDpocket: open-source cavity detection and characterization on molecular dynamics trajectories

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Solution structure of the sulfite reductase flavodoxin-like domain from Escherichia coli.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Untangling heavy protein and cofactor isotope effects on enzyme- catalyzed hydride transfer.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Substrate scope and selectivity in offspring to an enzyme subjected to directed evolution.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamic structures of horse liver alcohol dehydrogenase (HLADH): results of molecular dynamics simulations of HLADH-NAD(+)-PhCH(2)OH, HLADH-NAD(+)-PhCH(2)O(-), and HLADH-NADH-PhCHO.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Cofactor-Mediated Conformational Dynamics Promote Product Release From Escherichia coli Dihydrofolate Reductase via an Allosteric Pathway.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The dynamic energy landscape of dihydrofolate reductase catalysis

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamics of protein folding and cofactor binding monitored by single-molecule force spectroscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Calcium-dependent folding of single calmodulin molecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Conformational heterogeneity of the calmodulin binding interface.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

How do cofactors modulate protein folding?

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Role of cofactors in metalloprotein folding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Markov state models of biomolecular conformational dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein-protein interactions at an enzyme-substrate interface: characterization of transient reaction intermediates throughout a full catalytic cycle of Escherichia coli thioredoxin reductase.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Allosteric regulation and catalysis emerge via a common route.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Solution NMR Spectroscopy for the Study of Enzyme Allostery

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Protein Allostery and Conformational Dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Energy landscape views for interplays among folding, binding, and allostery of calmodulin domains.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamic Modelling Reveals 'Hotspots' on the Pathway to Enzyme-Substrate Complex Formation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Two pathways mediate interdomain allosteric regulation in pin1

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Dynamical network of residue-residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Principal component analysis: a method for determining the essential dynamics of proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Markov state models provide insights into dynamic modulation of protein function

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Transition-path theory and path-finding algorithms for the study of rare events

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Transition networks for modeling the kinetics of conformational change in macromolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Enhanced sampling techniques in molecular dynamics simulations of biological systems

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Molecular dynamics-based approaches for enhanced sampling of long-time, large-scale conformational changes in biomolecules

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Free energy calculations and ligand binding

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The linear interaction energy method for predicting ligand binding free energies

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

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

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

Water-protein interactions: the secret of protein dynamics

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FCATAL7070212

A new method for predicting binding affinity in computer-aided drug design

21 January 2018

1 reference

12 December 2020

Structural evidence for an anion-directing track in the hen ovotransferrin N-lobe: implications for transferrin synergistic anion binding

1 reference

12 December 2020

Water penetration and escape in proteins

1 reference

12 December 2020

Large-scale networks of hydration water molecules around proteins investigated by cryogenic X-ray crystallography.

1 reference

12 December 2020

Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry.

1 reference

12 December 2020

A comparison of methods to compute the potential of mean force

1 reference

12 December 2020

Modeling hydration mechanisms of enzymes in nonpolar and polar organic solvents

1 reference

12 December 2020

Molecular modeling of hydration in drug design.

1 reference

12 December 2020

Dynamics of hydration water in proteins.

1 reference

12 December 2020

Computational enzymology

1 reference

12 December 2020

Free Energy Barriers for Escape of Water Molecules from Protein Hydration Layer

1 reference

12 December 2020

Effects of organic solvent and crystal water on γ-chymotrypsin in acetonitrile media: observations from molecular dynamics simulation and DFT calculation

1 reference

12 December 2020

Nature of protein-CO2 interactions as elucidated via molecular dynamics

1 reference

12 December 2020

Site-specific coupling of hydration water and protein flexibility studied in solution with ultrafast 2D-IR spectroscopy

1 reference

12 December 2020

Identifiers

DOI

10.3390/CATAL7070212

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

5 May 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:30464857%20AND%20SRC:MED&resulttype=core&format=json

5 May 2020

1 reference