Method Cue

This cue indicates the types of studies. Structural analyses, such as crystallography and NMR, gives us more direct observation for enzyme reactions, whereas computational studies only suggest possibilities, for which Certainty levels of events are annotated as “Probable”..

(experimental/computational) study/studies
(experimental/computational) analysis/analyses simulation(s)
(computational) simulation(s)
(computational or support/provide) model(s)

More concrete keywords are as follows:

The following cues are related to structural analyses including X-ray crystallography or NMR study:

structural analyse
structural and biochemical studies
structural and functional analyses
structures
structural basis
structural characterization
structural comparison
structural consequences
structural data
structural models
structural perturbation
structural studies
structural work
structurally
structurally characterized
structure
structure and function analysis
Detailed structural analysis
Structural analyses
Structural analysis
Structural basis
Structural comparison
Structural determinants
Structural studies
Structural study
defined in structure
Molecular structure
atomic and ultra-high resolution
atomic co-ordinates
atomic level
atomic resolution
atomic structure refinement

The following cues are X-ray crystallography:

structure of crystal
Structure at 2.5-A resolution
Structure determination
These structures
Structure
This structure
X-ray analysis
X-ray crystal structure
X-ray crystal structures
X-ray crystallographic analyses
X-ray crystallographic data
X-ray crystallographic structure
X-ray crystallographic studies
X-ray crystallographic study
X-ray crystallographic techniques
X-ray crystallography
X-ray data
X-ray diffraction
X-ray diffraction data
X-ray diffraction techniques
X-ray spectroscopic
X-ray structure
X-ray structure refinement and comparison
X-ray structures
X-ray work
x-ray crystallographic methods
x-ray crystallography
x-ray crystallography studies
x-ray structure
Crystal structure
Crystal structures
Crystallographic
Crystallographic analysis
Crystallographic evidence
Crystallographic structural analysis
Crystallographic structure
Crystallographic studies
crystal
crystal and molecular structure
crystal form
crystal forms
crystal habit
crystal soaking experiment
crystal structure
crystal structure data
crystal structures
crystalline
crystalline form
crystalline state
crystallization
crystallize in tetragonal and orthorhombic space groups
crystallized
crystallizes
crystallographic
crystallographic agreement factors
crystallographic analyses
crystallographic analysis
crystallographic assignments
crystallographic asymmetric unit
crystallographic data
crystallographic evidence
crystallographic refinement
crystallographic results
crystallographic structure
crystallographic studies
crystallographic study
crystallographically
crystallography
crystals
cocrystal structure
cocrystal structures
cocrystallization
cocrystallized
cocrystallizing
collecting data from crystals
this X-ray structure
three-dimensional coordinates
three-dimensional structure
three-dimensional structures
two crystal structures
two different monoclinic crystal lattices
small crystalline
solved structures
resolution structure
refined crystal structure
refined high-resolution crystal structure
room-temperature X-ray synchrotron data
static x-ray structure
High-resolution crystal structures
High-resolution structures
high-resolution complex structure
high-resolution crystal structure
high-resolution crystal structures
high-resolution structures
Proton-Induced x-ray Emission
PIXE
Refined structure
Restrained crystallographic refinement
analysis of crystal and molecular structures
anisotropic X-ray diffraction
anomalous scattering method
earlier crystallographic interpretation
known crystal structures

The following methods are those by NMR techniques:

(1)H NMR
(1)H-(15)N HSQC
(1)H-(15)N HSQC data
(1)H-(15)N NMR spectroscopy
(13)C NMR
(13)C distortionless enhancement by polarization transfer
DEPT
(15)N-kinetic isotope effects
(1H, 15N) heteronuclear multiple-quantum coherence (HMQC) experiments
13C NMR
13C NMR spectra
13C magnetic resonances
13C-NMR study
13C-NMR titrations
19F-NMR
19F-NMR resonance
1D NMR and 2D NOESY analyses
1H NMR
1H NMR monitoring
1H NMR spectrum
31P NMR
31P NMR analyses
31P NMR spectroscopy
two-dimensional 31P-31P COSY experiments
structural and biochemical NMR studies
proton NMR
proton NMR studies
liquid-state NMR
NMR
NMR results
NMR spectroscopic analyses
NMR spectroscopy
NMR study
one- and two-dimensional proton NMR spectroscopy
heteronuclear single quantum correlation
HSQC

The following studies are mass spectrometry:

ESI
ESI-MS-MS
ESMS
Electrospray mass spectrometry
tandem MS
tandem MS/MS analyses
tandem mass spectrometry
LC-ESI-tandem MS
LC/MS analyses
MS
MS-MS
Mass spectrometric analysis
electrospray ionization mass spectrometry
electrospray ionization mass spectrum
electrospray ionization triple quadrupole mass spectrometry
electrospray mass spectrometry
ion-spray mass spectrometry
mass spectrometric monitoring
mass spectrometry
daughter-ion spectrum

The following are kinetic analyses including isotopic effects:

Kinetic
Kinetic analyses
Kinetic analysis
Kinetic characterization
Kinetic isotope effect studies
KIE
KIEs
beta-deuterium KIEs
alpha-deuterium kinetic isotope effects
analyzed kinetically
Kinetic studies
isotope effect
isotope effect data
isotope effects
isotope exchange
isotope ratio mass spectrometer
kinetic
kinetic analyses
kinetic analysis
kinetic consequences
kinetic data
kinetic evaluation
kinetic evidence
kinetic investigation
kinetic isotope effect
kinetic isotope effect measurements
kinetic isotope effect results
kinetic isotope effects
kinetic results
kinetic studies
kinetic study
kinetically
kinetically observed
kinetics
kinetics studies
This kinetic outcome
solvent deuterium isotope effect
solvent deuterium isotope effects
solvent isotope effect
solvent isotope effects
solvent kinetic deuterium-isotope effect
solvent kinetic isotope effects
these enzymatic isotope effects
secondary alpha-deuterium KIE
secondary beta-deuterium KIEs
primary (13)C KIE
Isotope effect studies
Isotope effects
studies kinetic
subjected to detailed kinetic investigation
techniques kinetic
steady-state kinetic analyses
steady-state kinetic data
steady-state rate analysis
Multiple kinetic isotope effects
Primary deuterium kinetic isotope effects
intrinsic isotope effects
inverse beta-secondary isotope effects
measured kinetic isotope effects
measurement of heavy-atom isotope effects
Solvent deuterium kinetic isotope effects
Solvent isotope effect studies
Steady-state kinetic analysis
Steady-state kinetic assays
Steady-state kinetic experiments
Steady-state kinetics
pre-steady-state kinetic analyses
15N-KIE
18(V/K)nonbridge isotope effect
Beta-secondary and solvent deuterium kinetic isotope effects

The following is mutagenesis:

Mutagenesis
Mutagenesis experiments
Mutagenesis studies
Mutational analysis
Mutational studies
site-directed mutagenesis
site-directed mutagenesis studies
site-directed mutations
Site-directed mutagenesis
new mutational data
mutagenesis
mutagenesis experiments
mutagenesis techniques
mutation studies
mutational analysis
experimental mutagenesis results
experimental site-directed mutagenesis
Primary and tertiary structure
SIRAS
Spectroscopic analyses
Steady-state fluorescence titration data
Stereochemical analysis
absorption changes
atomic absorption analysis
biochemical characterization
biochemical studies
Genetic and biochemical studies
chemical evidence
chemical modification
chemical sequencing
classical enzymological studies
cloning
collision-induced fragmentation
comparing kinetic results
comparison
competitive method

The following ones are other spectroscopic analyses:

difference FTIR spectroscopic analysis
difference FTIR spectroscopy
difference Fourier map
electronic absorption properties
faint absorption
far UV CD spectra
near UV CD spectra
circular dichroism
circular dichroism spectroscopy
CD spectroscopic studies
first detailed biochemical study
fluorescence
fluorescence studies
fluorescent
UV absorption maxima
UV spectroscopic
UV–visible
Analysis of absorption spectra
spectral characterization
spectral probes
spectrophotometric analysis
spectrophotometric assay
spectrophotometrically
spectroscopic characterization
spectroscopic data
spectroscopically
stereochemical studies
empirical correlation of delta
enzymatically characterized
equilibrium perturbation
establishes kinetically
expression
functional studies
heavy-atom isotope effects
highly sensitive new kinetic assay
higher resolution structural information
intense absorption
liquid chromatography
HPLC
HPLC analysis
mechanistic study
minimal perturbation
molecular explanation
molecular replacement
molecular structure and comparison
multiple isomorphous replacement
multipole refinement
one-turnover kinetics
pH dependence studies
pH studies
pH titration study
pH-dependent kinetic analysis
pH-dependent kinetics
pH-dependent rate analysis
pH-dependent studies
peptic digests
potential energy surface
provides convenient model system for studies
single isomorphous replacement with anomalous scattering method
Multipole refinement
Analysis of this structure
Atomic structure
Bronsted analysis
Chemical evidence
Cryoquenching
Difference Fourier comparisons
Difference Fourier maps
electron paramagnetic resonance spectroscopy
EPR studies
stereoelectronic theory
stopped-flow UV/Vis spectrophotometry
stopped-flow kinetic measurements
stopped-flow studies
substrate depletion
techniques structural
tetragonal crystal form
tetrameric quaternary structure
thermodynamic results
truncation experiments
viscosity measurements
visible absorbance spectroscopy

The following methods are computational or theoretical ones:

ab initio calculations
ab initio quantum chemical calculations
ab initio quantum mechanical modeling
Ab initio and density functional calculations
approximate valence bond method
AVB
Calculations
calculated
calculated using DelPhi program
calculation
calculations
computational docking
computational site-directed mutagenesis
computationally docked
computer fitting
computer graphics
computer simulations
construction observed structure readily allows
conventional molecular dynamics
conventional, classical force field
allow construction detailed model
structural alignment methods
structure-based model
theoretical calculations
theoretical considerations
theoretical data
theoretical examination
theoretical pK(a) calculations
theoretical results
theoretical work
theoretically
provides model
classical molecular mechanics model
quantum chemistry
quantum mechanical modeling
quantum mechanics
quantum-classical molecular dynamics simulations
Quantum chemical calculations
Quantum mechanics
smaller models
This model
Two simulations
docked structures
density functional calculations
density functional theory
MD
MD simulation
MD simulations
MD studies
Model building
Modeling
Modeling studies
Modelling
Models
Molecular dynamic studies
Molecular dynamics simulations
long-term molecular dynamics simulation
Molecular mechanics calculations show
Molecular modeling
model
model building calculations
model-building studies
modeled
modelled
modelling
modelling studies
models
molecular dynamics simulation
molecular dynamics simulation techniques
molecular dynamics simulations
molecular dynamics study
molecular mechanics
molecular mechanics potential
molecular mechanics simulation techniques
molecular modeling
predicted earlier from crystal structures
predicted from crystal structures
predicted sequence
refined model
relative large models
search model
simulates well
simulations
Electrostatic calculations
Poisson-Boltzmann equation
polarizable continuum model
Simulated
Single point energy calculations
gas-phase calculations
energies calculated
in silico