bigram

This is a table of type bigram and their frequencies. Use it to search & browse the list to learn more about your study carrel.

bigram	frequency
amino acid	823
amino acids	729
secondary structure	525
molecular dynamics	354
protein structure	325
crystal structure	322
binding site	303
active site	293
secondary structures	280
binding sites	250
free energy	231
virtual screening	212
electron microscopy	204
conformational changes	197
protein structures	189
antimicrobial peptides	183
drug discovery	182
crystal structures	180
structure prediction	178
glutamic acid	175
biological activity	172
protein interactions	164
acid residues	157
plasma membrane	155
side chain	153
dynamics simulations	147
mass spectrometry	147
solid phase	147
membrane proteins	145
side chains	144
intrinsically disordered	135
antimicrobial activity	132
nmr spectroscopy	132
force field	130
drug design	130
circular dichroism	129
ray crystallography	128
peptide synthesis	128
rna secondary	127
hydrogen bonds	125
base pairs	122
rna structure	119
protein folding	117
tertiary structure	115
structural biology	115
important role	113
experimental data	112
small molecules	111
lipid bilayer	110
two different	108
data bank	107
negatively charged	107
intrinsic disorder	107
nucleic acids	105
results show	105
living cells	104
binding affinity	101
monte carlo	99
target protein	99
structure determination	99
affi nity	99
protein data	97
single molecule	97
escherichia coli	96
building blocks	96
ligand binding	95
cell membrane	95
hydrogen bonding	94
acid sequence	94
cell surface	93
hydrogen bond	92
wide range	91
light scattering	90
water molecules	90
molecular weight	90
nucleic acid	90
rna structures	89
present study	89
structural information	89
cell lines	88
ion channels	88
results suggest	88
local structures	88
protein complexes	87
atomic force	87
small molecule	87
md simulations	86
electrostatic interactions	86
binding proteins	85
cancer cells	85
high affinity	85
amyloid fibrils	85
antimicrobial peptide	85
kcal mol	85
lipid membranes	84
protein function	84
rna molecules	84
large number	84
highly conserved	84
molecular modeling	83
terminal domain	82
high resolution	81
base pair	81
binding pocket	81
disordered proteins	80
biologically active	80
gene expression	80
dimensional structure	79
force microscopy	79
sequence identity	78
lipid bilayers	78
sequence alignment	78
scanning electron	76
widely used	76
phase peptide	76
wild type	76
binding protein	75
magnetic resonance	75
membrane protein	75
modifi ed	75
window size	74
binding domain	74
cell adhesion	74
positively charged	71
structure elements	71
energy transfer	71
fi rst	70
protein binding	69
doc id	69
cord uid	69
molecular docking	69
key role	68
rna polymerase	68
structural data	68
protein interaction	68
structural features	68
signal transduction	67
molecular level	67
cell membranes	67
protein sequences	67
previous studies	66
idps idprs	66
ray diffraction	66
structural studies	66
transmission electron	66
structural basis	66
drug delivery	65
protein sequence	65
structural changes	65
results indicate	65
conformational change	65
fluorescence microscopy	64
terminal region	64
fluorescence spectroscopy	64
nuclear magnetic	64
electron microscope	64
biological processes	64
cyclic peptides	63
inhibitory activity	62
acute respiratory	61
electron density	61
structural analysis	61
atomic resolution	61
disulfide bonds	61
identifi ed	61
comparative modeling	60
fl uorescence	60
protein design	60
homology models	60
naturally occurring	60
results obtained	60
respiratory syndrome	60
computational methods	59
model system	59
acid sequences	59
protein engineering	59
molecular mechanisms	58
present work	58
nervous system	58
tertiary structures	57
van der	57
glutamic acids	56
molecular biology	56
severe acute	56
correlation spectroscopy	55
polypeptide chain	55
cellular processes	55
drug development	54
breast cancer	54
binding mode	54
closely related	53
phase synthesis	53
dimensional structures	53
fluorescent protein	53
tertiary interactions	53
active sites	53
cell death	53
effi cient	53
primary structure	52
electron beam	52
synthetic peptides	52
growth factor	52
activity relationship	52
ordered proteins	52
based drug	52
type i	52
protein complex	51
rna folding	51
host cell	51
modifi cation	51
first step	51
main protease	51
molecular mechanism	50
purifi cation	50
structural motifs	50
ray scattering	50
disulfide bridges	50
der waals	49
sequence similarity	49
disordered regions	49
tumor cells	49
cyclic peptide	49
nmr studies	49
also known	49
structure alignment	49
ab initio	48
conformational analysis	48
target proteins	48
enzymatic activity	48
molecular recognition	48
may also	47
first time	47
force fields	47
well known	47
biological functions	47
confocal microscopy	47
purifi ed	47
electron transfer	47
side effects	46
allowed us	46
aqueous solution	46
directed mutagenesis	46
ionic strength	46
specifi city	46
recent years	45
central nervous	45
receptor binding	45
acid composition	45
biological function	45
calculated using	45
dynamic light	45
cancer cell	45
commonly used	45
viral rna	45
titration calorimetry	45
different types	45
peptides containing	45
will present	45
ion channel	45
rna sequences	45
acid residue	45
protein surface	45
mammalian cells	44
rational design	44
structural elements	44
protein families	44
signifi cant	44
homology model	44
isothermal titration	44
results showed	44
transcription factor	44
chemical shift	43
web server	43
peptide sequences	43
dna binding	43
social networks	43
negative bacteria	43
better understanding	43
cell types	42
infl uence	42
coiled coil	42
immune response	42
peptide sequence	42
cell cycle	42
i will	42
energy functions	42
viral replication	42
amino group	42
metal ions	42
starting point	42
fluorescence correlation	42
also observed	42
functional groups	42
free energies	42
surface plasmon	41
immunodeficiency virus	41
charged residues	41
homology modeling	41
transcription factors	41
lipid membrane	41
three different	41
cell proliferation	41
using molecular	41
comparative models	41
biological membranes	41
data suggest	41
sequence information	41
based methods	41
membrane fusion	41
oxidative stress	41
biological systems	41
physiological conditions	41
extracellular matrix	41
em structure	41
room temperature	41
catalytic domain	40
performed using	40
energy function	40
model membranes	40
powerful tool	40
rna molecule	40
type ii	40
peptide chain	40
two types	39
immune system	39
prostate cancer	39
cell biology	39
even though	39
amyloid formation	39
penetrating peptides	39
physicochemical properties	39
molecular mechanics	39
synthetic peptide	39
serine protease	39
helical structure	39
natural products	39
thermal stability	39
human diseases	39
recent studies	39
disulfide bond	39
modifi cations	38
fatty acid	38
dependent manner	38
plasmon resonance	38
complex formation	38
eukaryotic cells	38
outer membrane	38
dependent rna	38
full length	38
structural folds	38
ray structure	38
phage display	38
activity relationships	38
neurodegenerative diseases	38
peptides derived	38
structural characterization	38
interaction energy	38
enzyme activity	37
molecular interactions	37
high throughput	37
therapeutic agents	37
functionally important	37
protein aggregation	37
loop regions	37
cell penetrating	37
also found	37
neural network	37
new class	37
experimentally determined	37
fibril formation	37
structural properties	37
different proteins	37
mechanical properties	37
chemical synthesis	37
sequence space	37
pdb id	37
aromatic residues	37
binding properties	37
net charge	37
model systems	37
pharmacophore model	36
laser scanning	36
binding partners	36
cell wall	36
human immunodeficiency	36
solid support	36
human genome	36
effi ciency	36
gel electrophoresis	36
nmr data	36
cell line	36
catalytic activity	36
metal ion	36
template structure	36
scoring function	36
main proteinase	36
disordered protein	36
carbohydrate binding	36
live cells	36
bioactive peptides	36
biological activities	35
protein dynamics	35
fluorescent proteins	35
bond formation	35
allows us	35
scoring functions	35
will allow	35
sh domain	35
spike protein	35
vp vp	35
molten globule	35
unilamellar vesicles	35
fold recognition	35
surface area	35
life cycle	34
structure analysis	34
identifi cation	34
amide bond	34
protein synthesis	34
functional sites	34
helical conformation	34
experimental results	34
resonance energy	34
also used	34
crucial role	34
normal mode	34
related proteins	34
cross section	34
novo design	34
proteins involved	34
molecular basis	34
antiviral activity	33
specifi cally	33
peptide analogues	33
drug target	33
small angle	33
electrostatic potential	33
simulated annealing	33
least one	33
protein kinase	33
results provide	33
poorly understood	33
endothelial cells	33
two distinct	33
sars coronavirus	33
chain length	33
eudoc program	33
protease inhibitors	33
new method	33
silico pharmacology	33
helical regions	33
chemical properties	33
reverse transcriptase	33
photosystem ii	33
using different	32
lipid composition	32
protein molecules	32
cell division	32
native structure	32
clinical trials	32
exclusion chromatography	32
structural similarity	32
rna viruses	32
takes place	32
bacillus subtilis	32
molecular modelling	32
structure information	32
data obtained	32
physical properties	32
structure fragments	32
two proteins	32
commercially available	32
dynamic programming	32
active peptides	32
cysteine residues	32
conformational space	32
natively unfolded	32
mosaic virus	32
taken together	32
aspartic acid	32
recent advances	32
protein threading	32
least two	32
blood pressure	32
short peptides	31
mg ml	31
hydrophobic interactions	31
new insights	31
multiple sequence	31
coupled receptors	31
computational approaches	31
local structure	31
human cells	31
native state	31
nmr experiments	31
low energy	31
chemical shifts	31
peptide backbone	31
chemical ligation	31
ebola virus	31
drug candidates	31
nmr spectra	31
enveloped viruses	30
signaling pathways	30
peptide bond	30
fl uorescent	30
conformational states	30
wide variety	30
tree decomposition	30
based pharmacophore	30
derived peptides	30
phase transition	30
serine proteases	30
peptide ligands	30
based approach	30
stranded dna	30
protein functions	30
using nmr	30
studies showed	30
platelet aggregation	30
tyrosine kinase	30
genomic rna	30
peptide design	30
dynamics simulation	30
multiple sclerosis	30
quaternary structure	30
conformational flexibility	30
capsid protein	30
cd spectroscopy	30
cellular uptake	30
data show	30
liquid chromatography	30
semv protease	30
take place	30
like structures	30
metal binding	30
chemical descriptors	30
previously reported	30
substrate specificity	29
target sequence	29
torsion angles	29
molecular structure	29
based virtual	29
protecting groups	29
metabolic stability	29
differential scanning	29
ray crystal	29
large rna	29
investigated using	29
based design	29
unnatural amino	29
base pairing	29
resolution structure	29
two main	29
confocal laser	29
atomic level	29
helix bundle	29
oxygen species	29
sequence alignments	29
internal loops	29
diffi cult	29
time scale	29
gene delivery	29
substrate binding	29
may lead	29
new approach	29
experimental conditions	28
random coil	28
will show	28
major groove	28
results demonstrate	28
point mutations	28
binding affinities	28
distance cutoff	28
peptide library	28
cross sections	28
reactive oxygen	28
fluorescence intensity	28
nmr structure	28
scanning vol	28
studied using	28
stem cells	28
integral membrane	28
carboxylic acid	28
supplement iv	28
estrogen receptor	28
fatty acids	28
determined using	28
containing peptides	28
recently developed	28
binding modes	28
transition state	28
partition coefficient	28
hairpin loops	28
acid side	28
energy minimization	28
three dimensional	28
native chemical	28
protein fold	28
crystal packing	28
interaction sites	27
using fmoc	27
specific binding	27
solution structure	27
currently used	27
good agreement	27
structural models	27
data analysis	27
ray structures	27
better understand	27
large scale	27
unpaired nucleotides	27
molecule fluorescence	27
size exclusion	27
data set	27
membrane interaction	27
recently reported	27
dna sequences	27
active compounds	27
hydrophobic core	27
carbohydrate structure	27
analysis revealed	27
biological properties	27
cys residues	27
prion protein	27
peptide fragments	27
proteins may	27
potential therapeutic	27
space group	27
sequence analysis	27
many different	26
drug targets	26
binding free	26
query sequence	26
mean square	26
throughput screening	26
model peptides	26
allow us	26
main chain	26
structural proteins	26
light microscopy	26
newly synthesized	26
peptide binding	26
host cells	26
fluorescence lifetime	26
membrane surface	26
delivery systems	26
cell culture	26
coupling reagents	26
high affi	26
fourier transform	26
saccharomyces cerevisiae	26
signifi cantly	26
major role	26
like peptides	26
structure motifs	26
diffraction data	26
potential energy	26
potent inhibitors	26
structure modeling	26
peptide libraries	26
novel approach	26
structures using	26
ligand interactions	26
molecular mass	26
real time	26
previous work	25
red blood	25
assembly process	25
rich domains	25
aqueous solutions	25
low molecular	25
new analogues	25
novel coronavirus	25
folding process	25
docking studies	25
ligand docking	25
terminal part	25
opioid receptor	25
will also	25
small number	25
many cases	25
complex structures	25
terminal residues	25
sh domains	25
high degree	25
positional hits	25
threading problem	25
membrane potential	25
training set	25
critical role	25
neural networks	25
building block	25
rna replication	25
autoimmune diseases	25
ray crystallographic	25
bulge loops	24
minor groove	24
positive charge	24
limited number	24
large rnas	24
primary sequence	24
neutron scattering	24
bacterial membranes	24
endoplasmic reticulum	24
network size	24
serum albumin	24
data sets	24
confi rmed	24
cell growth	24
functional proteins	24
carbohydrate structures	24
like protease	24
solvent accessibility	24
dipartimento di	24
mg kg	24
sequence variability	24
rdrp suppl	24
energy landscape	24
protein stability	24
may provide	24
staphylococcus aureus	24
acidic ph	24
sheet structures	24
studies revealed	24
scanning calorimetry	24
fusion protein	24
state nmr	24
minimum energy	24
protein structural	24
brain barrier	24
innate immunity	24
dengue virus	24
physical chemistry	24
determine whether	24
structural motif	24
single protein	24
data determined	24
skeletal muscle	24
proline residues	23
protein chain	23
hydrogen atoms	23
previously described	23
blood cells	23
monoclonal antibodies	23
raman spectroscopy	23
coronavirus main	23
will provide	23
peptide conjugates	23
protein coupled	23
sample preparation	23
catalytic site	23
fi brils	23
selected compounds	23
biological material	23
essential role	23
protease activity	23
specific interactions	23
provide new	23
reaction center	23
atpase activity	23
membrane lipids	23
protein family	23
pharmacophore models	23
candida albicans	23
quantitative structure	23
protein secondary	23
terminal amino	23
double helix	23
native peptide	23
two peptides	23
low temperature	23
force spectroscopy	23
optical tweezers	23
molecular dynamic	23
physiological ph	23
similarity score	23
protease domain	23
affinity chromatography	23
stranded rna	23
protein degradation	23
prediction methods	23
long time	23
highly potent	23
two domains	23
like protein	23
several different	23
positive bacteria	23
binding domains	23
antifungal activity	23
assembled structures	23
noise ratio	23
threading programs	23
innate immune	22
dna sequence	22
suppl table	22
protein domains	22
peptide structures	22
structure element	22
structures formed	22
broad spectrum	22
fluorescent probes	22
known protein	22
domain swapping	22
see table	22
calcium binding	22
using fluorescence	22
resolution structures	22
amyloid aggregation	22
method using	22
experimental studies	22
financial support	22
structure formation	22
rheumatoid arthritis	22
hiv protease	22
syndrome coronavirus	22
conformational transition	22
protein interfaces	22
structural genomics	22
may play	22
discovery process	22
atomic coordinates	22
data collection	22
important roles	22
amino groups	22
structural database	22
scanning microscopy	22
years ago	22
viral genome	22
water interface	22
lipid vesicles	22
obtained results	22
different cell	22
using two	22
hydrophobic interaction	22
conformational properties	22
analyzed using	22
green fluorescent	22
drug repurposing	22
like proteins	22
analysis showed	22
surface charge	22
asymmetric unit	22
rna structural	22
binding pockets	22
cellular functions	22
functional properties	22
biologically relevant	21
ms ms	21
unfolded state	21
proton transfer	21
experiments showed	21
nucleotide binding	21
higher affinity	21
cell entry	21
tumor cell	21
organic solvents	21
stacking interactions	21
last years	21
fmoc tbu	21
radiation damage	21
results will	21
transmembrane domain	21
also performed	21
synthesized using	21
molecule level	21
protein flexibility	21
state university	21
solid state	21
sequence homology	21
chemical stability	21
complex structure	21
model based	21
infrared spectroscopy	21
protein fragments	21
different protein	21
hydrophobic residues	21
graduate school	21
protein kinases	21
like domain	21
conformational studies	21
lipid rafts	21
antibacterial activity	21
binding process	21
hydration water	21
terminal fragment	21
peptide nanostructures	21
cell migration	21
kinetic parameters	21
defi ned	21
recent work	21
highly selective	21
virus type	21
arginine residues	21
class i	21
silico screening	21
quality control	21
broad range	21
triple helix	21
protein targets	21
one another	21
based therapeutics	21
therapeutic target	21
partially folded	21
structure database	21
specific functions	21
low concentrations	21
much less	21
translational modification	21
single particle	21
water molecule	21
much higher	21
translational modifications	21
aggregation process	21
human plasma	20
physiological processes	20
binding motif	20
ang ii	20
medicinal chemistry	20
soluble proteins	20
local structural	20
vivo studies	20
protein molecule	20
influenza virus	20
human amps	20
preliminary results	20
distance matrix	20
shed light	20
biophysical chemistry	20
globular proteins	20
rate constants	20
relatively small	20
drug resistance	20
image processing	20
immune responses	20
like structure	20
temperature range	20
zn sites	20
nucleocapsid protein	20
combinatorial chemistry	20
inhibitory effect	20
hela cells	20
artifi cial	20
peptide derivatives	20
functional protein	20
binding kinetics	20
islet amyloid	20
synthesis using	20
tumor growth	20
latent space	20
trypsin inhibitor	20
explicit solvent	20
target cells	20
natural amino	20
ligand complexes	20
domain ii	20
ser thr	20
actin cytoskeleton	20
redox pairs	20
optical microscopy	20
residues involved	20
electron tomography	20
amyloid fibril	20
comparative protein	20
ftir spectroscopy	20
amyloid peptide	20
fold higher	20
fully understood	20
group ii	20
gene therapy	20
bacterial cell	20
electron microscopic	20
biological macromolecules	20
functional group	20
dna repair	20
many proteins	20
peptide structure	20
high concentration	20
sheet structure	20
two sequences	20
form amyloid	20
backbone atoms	20
protein science	20
dihydrofolate reductase	20
virus particles	20
also investigated	20
capsid proteins	19
rna interactions	19
phosphate groups	19
obtained using	19
flexible motion	19
cell walls	19
machine learning	19
electron micrographs	19
structural model	19
give rise	19
ph values	19
fluorescence anisotropy	19
results indicated	19
pore formation	19
acyl chain	19
assembled peptide	19
based protein	19
comparative analysis	19
protein docking	19
potent inhibitor	19
cysteine proteases	19
acid derivatives	19
cho cells	19
blood coagulation	19
different methods	19
supported lipid	19
computational tools	19
gives rise	19
charged amino	19
model membrane	19
protein backbone	19
human serum	19
disulfide bridge	19
great interest	19
contains two	19
human body	19
dna damage	19
helical structures	19
proteins containing	19
distance geometry	19
neutral ph	19
rna sequence	19
novel peptide	19
opioid receptors	19
delivery system	19
istituto di	19
cd spectra	19
potassium channel	19
human igg	19
epithelial cells	19
viral proteins	19
sequence motifs	19
computational design	19
past years	19
biophysical techniques	19
still unclear	19
posttranslational modifications	19
cellular membranes	19
host complexes	19
precursor protein	19
torsion angle	19
conformational preferences	19
fi eld	19
known structure	19
structural stability	19
native protein	19
heparan sulfate	19
phase method	19
protein tyrosine	19
nmr structures	19
fragment screening	19
antiviral drug	19
tumor suppressor	19
dna replication	19
unfolded proteins	19
low resolution	19
high level	19
intermolecular interactions	19
blood vessels	19
covalent bonds	19
energy conformations	19
dissociation constant	19
protein disorder	19
membrane permeability	19
great potential	19
lead compounds	19
pair similarity	19
spatial resolution	19
amber force	19
functional importance	19
protein unfolding	19
excited state	19
redox activity	19
image analysis	19
hairpin loop	18
protein aggregates	18
silico methods	18
large amounts	18
proteins using	18
poliovirus rdrp	18
high levels	18
nuclear receptor	18
catalytic mechanism	18
protecting group	18
based method	18
alpha helices	18
specific amino	18
experimental evidence	18
lipid interactions	18
life sciences	18
four different	18
binding studies	18
protein intrinsic	18
rna binding	18
synchrotron radiation	18
photodynamic therapy	18
muscle cells	18
angiotensin ii	18
biological samples	18
interacting proteins	18
fi nal	18
catalytic residues	18
vast majority	18
structure similarity	18
early stages	18
like particles	18
many biological	18
protein misfolding	18
structural protein	18
signi cant	18
actin filaments	18
structure based	18
biomedical applications	18
channel activity	18
molecule inhibitors	18
diseases including	18
enzyme active	18
low micromolar	18
evaluated using	18
time resolution	18
possible role	18
useful tool	18
ic values	18
bound state	18
cell imaging	18
protease inhibitor	18
rich sequences	18
also shown	18
infected cells	18
conserved residues	18
based approaches	18
aided design	18
dna polymerase	18
optical properties	18
electrostatic interaction	18
expressed protein	18
aromatic ring	18
animal models	18
important residues	18
tryptophan residues	18
heat shock	18
highly specific	18
analysis using	18
chemical structure	18
amyloid polypeptide	18
dihedral angles	18
highly significant	18
prior knowledge	18
covalently linked	18
currently available	18
query protein	18
living organisms	18
bovine serum	17
lattice structure	17
extensively studied	17
catalytic efficiency	17
multidrug resistance	17
kagome lattice	17
successfully applied	17
bond lengths	17
coupling reaction	17
imaging techniques	17
threading alignment	17
time resolved	17
temperature dependence	17
pseudomonas aeruginosa	17
phosphate backbone	17
small size	17
less stable	17
support vector	17
organic compounds	17
tandem mass	17
membrane binding	17
pharmacophore modeling	17
chemical modification	17
methods used	17
peptide nanotubes	17
increasing number	17
steric hindrance	17
fully automated	17
high yield	17
singlet oxygen	17
complex i	17
well established	17
nucleotide sequence	17
predicting protein	17
membrane interactions	17
plasmodium falciparum	17
microscopy techniques	17
icosahedral symmetry	17
college london	17
binding peptides	17
molecular structures	17
low affinity	17
anticodon loop	17
research center	17
synthesized peptides	17
inflammatory drugs	17
peptide amphiphiles	17
lipid peroxidation	17
well understood	17
quantitative analysis	17
temporal resolution	17
salt concentrations	17
binding affi	17
different conformations	17
giant unilamellar	17
rich peptides	17
linear peptide	17
achieved using	17
ray data	17
genetic code	17
potential drug	17
different lipid	17
also showed	17
polypeptide chains	17
useful tools	17
previous study	17
well defined	17
type protein	17
particular interest	17
gene encoding	17
therapeutic potential	17
intrinsically unstructured	17
proteolytic degradation	17
cell signaling	17
natural compounds	17
promising candidates	17
therapeutic strategies	17
times higher	17
enabled us	17
peptide molecules	17
structure models	17
water soluble	17
template structures	17
known structures	17
rich protein	17
higher plants	17
located within	17
terminal helix	17
function relationship	17
model peptide	17
hydroxyl group	17
peptide derived	17
macro level	17
highly flexible	17
ng ml	17
may contribute	17
transition temperature	17
rigid cluster	17
ribosomal subunit	17
vice versa	17
peptide concentration	17
key step	17
live cell	17
database searching	17
group i	17
peptides corresponding	16
spatial distribution	16
measured using	16
function relationships	16
quantum dots	16
crystallographic structures	16
gibbs free	16
conformational stability	16
local alignment	16
secondary electron	16
single molecules	16
prediction using	16
rational drug	16
nuclear receptors	16
protein ligation	16
also studied	16
cysteine protease	16
protein conformational	16
hcv ns	16
reverse transcription	16
binding activity	16
antiproliferative activity	16
renin inhibitors	16
high content	16
density maps	16
experimental methods	16
driving force	16
micromolar range	16
detailed analysis	16
elastic network	16
model building	16
divalent cations	16
various proteins	16
covalently bound	16
planck institute	16
amyloid beta	16
molar ratio	16
based prediction	16
viral life	16
coupled receptor	16
critical assessment	16
common structural	16
play important	16
group size	16
different conditions	16
peptide chains	16
high pressure	16
cell type	16
biophysical properties	16
mott cross	16
remains unclear	16
sars virus	16
ordered structure	16
structurally related	16
action potential	16
protein surfaces	16
resolved fluorescence	16
fluorescently labeled	16
results also	16
natural product	16
electric field	16
homology modelling	16
energy model	16
using circular	16
predicted structures	16
peptide docking	16
cancer therapy	16
will discuss	16
assembling peptide	16
current study	16
rna genome	16
using computational	16
rna pseudoknots	16
profi le	16
mm nacl	16
reference structure	16
macromolecular structures	16
approach based	16
alpha helix	16
czech republic	16
studies will	16
optimal threading	16
adrenergic receptor	16
secondary metabolites	16
receptor antagonists	16
cationic antimicrobial	16
recombinant proteins	16
fluorescence emission	16
potential target	16
new inhibitors	16
last decade	16
taking advantage	16
structures based	16
evidence suggests	16
structures determined	16
rationally designed	16
conformational dynamics	16
detailed structural	16
lead discovery	16
structure activity	16
protein domain	16
folded proteins	16
acid peptide	16
pdb code	16
three domains	16
homologous proteins	16
previously shown	16
stem loop	16
host defense	16
therapeutic agent	16
protein expression	16
secondary structural	16
two methods	16
hairpin structure	16
based model	16
signaling pathway	16
spike glycoprotein	16
uorescence spectroscopy	16
tree width	16
mutation rate	16
kda protein	16
magnetic field	16
backbone conformations	16
qm mm	15
binding region	15
membrane tension	15
hydrophobic amino	15
peptide chemistry	15
functional studies	15
order disorder	15
fibrillar aggregates	15
spectroscopic techniques	15
performance liquid	15
molecular weights	15
md simulation	15
transform infrared	15
various biological	15
valuable information	15
acetic acid	15
genetic information	15
also show	15
absorption spectroscopy	15
data processing	15
terminal sequence	15
site residues	15
low ph	15
small peptides	15
two hydrogen	15
experiments show	15
di fisica	15
phylogenetic comparison	15
human coronavirus	15
results revealed	15
highly dynamic	15
square deviation	15
three dimensions	15
native proteins	15
dna complexes	15
size values	15
environmental conditions	15
two important	15
redox states	15
organic molecules	15
binding specificity	15
adhesion molecules	15
different ph	15
lysine residues	15
analytical ultracentrifugation	15
strictly conserved	15
redox pair	15
gated ion	15
may result	15
effi ciently	15
highly efficient	15
structures may	15
parameter set	15
fluorescence quenching	15
blood plasma	15
signal peptide	15
close proximity	15
geometric simulation	15
peptide analogs	15
new therapeutic	15
like peptide	15
organic solvent	15
prepared using	15
energy calculations	15
pharmacokinetic properties	15
hydrogen peroxide	15
high concentrations	15
vero cells	15
per residue	15
folding model	15
cleavage sites	15
using single	15
supramolecular structures	15
next step	15
gram negative	15
biological sciences	15
active conformation	15
hemolytic activity	15
coil structure	15
fluid phase	15
membrane structure	15
scanning probe	15
open reading	15
signalling pathways	15
local regions	15
national institute	15
structure model	15
lipid transfer	15
resonance spectroscopy	15
systems biology	15
infectious diseases	15
score values	15
different strategies	15
phase separation	15
novel inhibitors	15
among others	15
supporting information	15
short peptide	15
peptide fragment	15
flow cytometry	15
cell viability	15
different structural	15
food intake	15
root mean	15
functional domains	15
click chemistry	15
nmr methods	15
free radical	15
docking methods	15
acyl chains	15
nmr techniques	15
solution structures	15
present results	15
class ii	15
also provides	15
united states	15
pdb entries	15
carlo simulation	15
alternative splicing	15
much larger	15
peptide bonds	15
structural alignment	15
integer programming	15
protein conformation	15
one hand	15
new family	15
new drugs	15
negative charge	14
na ions	14
virus inactivation	14
promising approach	14
ribosomal rna	14
computational protein	14
new type	14
cell differentiation	14
different structures	14
flexible docking	14
recent developments	14
important structural	14
conformational behavior	14
specific proteins	14
model protein	14
structural classification	14
two decades	14
terminal end	14
surface receptors	14
experimental techniques	14
human social	14
wound healing	14
protein interface	14
light harvesting	14
direct interaction	14
linear peptides	14
new peptides	14
fluorescence resonance	14
viral proteases	14
significantly different	14
mode analysis	14
science foundation	14
structural determinants	14
successfully used	14
computer simulations	14
structural organization	14
force microscope	14
domain iii	14
carbohydrate moiety	14
peptide interactions	14
stem cell	14
spinal cord	14
significant role	14
computer simulation	14
network model	14
biological effects	14
aqueous media	14
high specificity	14
ga iv	14
san diego	14
thermal unfolding	14
early stage	14
protein concentration	14
raw data	14
dynamics studies	14
specific residues	14
dynamic simulations	14
repeat proteins	14
potential use	14
determined structures	14
chemical modifications	14
data acquisition	14
italian institute	14
single point	14
extended idps	14
covalent bond	14
stable structure	14
gold nanoparticles	14
biologically important	14
hyaluronic acid	14
em structures	14
mutational analysis	14
gram positive	14
sodium channel	14
membrane receptors	14
rat brain	14
ca binding	14
posttranslational modification	14
light chain	14
recombinant protein	14
significantly higher	14
rich region	14
elastic modulus	14
central role	14
molecular motors	14
intermolecular interaction	14
new structure	14
human host	14
chemical composition	14
trichogin ga	14
approach using	14
converting enzyme	14
clinical studies	14
different conformational	14
predict protein	14
moderately active	14
table i	14
kj mol	14
high performance	14
prediction programs	14
different temperatures	14
ii diabetes	14
range interactions	14
plant amps	14
structural differences	14
enzymatic degradation	14
using various	14
confi guration	14
atom molecular	14
single sequence	14
database search	14
specific interaction	14
point mutation	14
respiratory chain	14
high temperature	14
cell receptor	14
first one	14
cryoelectron microscopy	14
containing two	14
novel method	14
may act	14
structural dynamics	14
thylakoid membranes	14
atp binding	14
structurally diverse	14
protein folds	14
nuclear overhauser	14
partition function	14
protonation states	14
highly sensitive	14
chemical structures	14
peptide self	14
based screening	14
binding assay	14
low sequence	14
many viruses	14
work will	14
control group	14
carlo simulations	14
therapeutic applications	14
computational study	14
kinase inhibitors	14
vitro studies	14
crystal forms	14
showed high	14
simple model	14
provide insight	14
highly active	14
herpes simplex	14
active molecules	14
bioactive conformation	14
family members	14
physiologically relevant	14
microwave assisted	14
trp residues	14
may represent	14
bacterial growth	14
high efficiency	13
density map	13
will give	13
binding partner	13
will describe	13
induced fit	13
patch clamp	13
conformational transitions	13
also able	13
natural ligand	13
thermodynamic parameters	13
large unilamellar	13
also possible	13
bacterial membrane	13
electron paramagnetic	13
different positions	13
small protein	13
well characterized	13
domain i	13
peptide nucleic	13
single molecular	13
cystine knot	13
loop structures	13
powerful technique	13
large numbers	13
single channel	13
aspartic acids	13
several examples	13
high purity	13
different amino	13
zinc ion	13
vascular endothelial	13
reading frame	13
also demonstrated	13
nucleotide sequences	13
significant effect	13
human cancer	13
major histocompatibility	13
residues located	13
fl ow	13
specific protein	13
light source	13
electrostatic repulsion	13
dissociation constants	13
carbonic anhydrase	13
binding assays	13
charge density	13
correlation analysis	13
human breast	13
like receptor	13
rna virus	13
receptor protein	13
residue correspondences	13
two kinds	13
similar structures	13
two steps	13
native conformation	13
one example	13
backbone interactions	13
research group	13
structure graph	13
fluorescence techniques	13
sequence conservation	13
public health	13
proton pump	13
statistical significance	13
step towards	13
nitric oxide	13
chemical probing	13
lmqc structures	13
computer programs	13
human rhinovirus	13
peptides may	13
proteolytic enzymes	13
steady state	13
distance constraints	13
potassium channels	13
low toxicity	13
size distribution	13
peptide conformation	13
well suited	13
phosphate buffer	13
induced conformational	13
dimer interface	13
drug molecules	13
nanomolar range	13
activity studies	13
negative staining	13
ap activity	13
transmembrane region	13
large conformational	13
enzyme inhibitors	13
biophysical methods	13
energy term	13
electron transport	13
positive charges	13
transmembrane protein	13
high selectivity	13
distantly related	13
free amino	13
intermolecular disulfide	13
globule state	13
physiological functions	13
affi nities	13
fluorescent molecules	13
disulfide redox	13
chemically synthesized	13
social network	13
residues within	13
transmembrane domains	13
carbohydrate complexes	13
fusion peptide	13
membrane curvature	13
comparative study	13
develop new	13
based energy	13
experimental structures	13
major structural	13
major challenge	13
common feature	13
cyclic nucleotide	13
cysteine residue	13
arabidopsis thaliana	13
quantum mechanics	13
octanol water	13
commonly found	13
gp spike	13
design using	13
tyrosine kinases	13
proteins within	13
relatively large	13
transmembrane proteins	13
may serve	13
unstructured proteins	13
different stages	13
diffusion coefficient	13
fluorescence spectra	13
affinity energy	13
molecular surface	13
beta peptide	13
neutral networks	13
second step	13
lifetime imaging	13
changes associated	13
prediction accuracy	13
pivot molecule	13
complexes formed	13
viral families	13
similarity scores	13
carboxyl group	13
lipid molecules	13
significant linear	13
disordered region	13
confocal microscope	13
several proteins	13
might also	13
cell cultures	13
peptide arrays	13
genetically encoded	13
binding energy	13
function prediction	13
crystallographic data	13
anticancer drugs	13
polyethylene glycol	13
dielectric constant	13
functional annotation	13
hot spots	13
provide insights	13
ramachandran plot	13
cov main	13
fmoc chemistry	13
peptide inhibitors	13
matrix protein	13
individual proteins	13
promoting residues	13
viral entry	13
will help	13
monoclonal antibody	13
drug leads	13
carbohydrate molecules	13
mean force	13
based scoring	13
particle size	13
dn pv	13
protein identification	13
pseudoknot prediction	13
well studied	13
virtual hits	13
redox regulation	13
salt bridges	13
selected structures	13
particularly interesting	13
results reveal	13
single stranded	13
structure predictions	13
functional characteristics	13
quantum chemical	13
small proteins	13
also present	13
atomic structure	13
comparative model	13
related diseases	13
protein chains	13
presentation will	13
muscle contraction	13
thermal denaturation	13
great importance	13
paramagnetic resonance	12
three types	12
limiting step	12
icosahedral viruses	12
peptide dendrimers	12
mutation rates	12
key residues	12
glycosidic bond	12
accessible surface	12
least three	12
unit cell	12
throughput docking	12
low concentration	12
inflammatory diseases	12
antiviral drugs	12
often used	12
dna molecules	12
special attention	12
similar results	12
folded protein	12
bound protein	12
predicted secondary	12
three major	12
peripheral blood	12
new generation	12
conventional antibiotics	12
redox state	12
crystal form	12
threedimensional structure	12
emission spectra	12
relatively short	12
sequence seq	12
chain conformations	12
brownian dynamics	12
sars cov	12
many physiological	12
derived peptide	12
rna pseudoknot	12
protein local	12
high molecular	12
functional role	12
receptor tyrosine	12
dynamic properties	12
optimal structure	12
also includes	12
using high	12
biological research	12
clementsian structure	12
penetrating peptide	12
extended conformation	12
like molecules	12
computational studies	12
terminal domains	12
molecule force	12
protein models	12
structural requirements	12
bioactive compounds	12
sialic acid	12
plasmid dna	12
still unknown	12
data indicate	12
scaffold proteins	12
several methods	12
selectivity filter	12
glutamate receptors	12
new potential	12
results may	12
another important	12
structural rearrangements	12
ligand bound	12
new insight	12
wistar rats	12
functional elements	12
molecular biophysics	12
virulence factors	12
recent research	12
studies indicate	12
prediction method	12
structurally characterized	12
structural positions	12
coupling constants	12
gene regulation	12
gene ontology	12
viral envelope	12
three distinct	12
laser desorption	12
structure validation	12
neurodegenerative disorders	12
micro level	12
phase ii	12
viral infection	12
built using	12
surface topography	12
cellular membrane	12
isoelectric point	12
head groups	12
scattering cross	12
terminal peptide	12
distance matrices	12
harvesting complex	12
acidic residues	12
human disease	12
basic idea	12
crick base	12
aminoisobutyric acid	12
redox potential	12
proteins will	12
apo form	12
proteolytic stability	12
ir absorption	12
success rate	12
mathematical model	12
potentially useful	12
specific antibodies	12
many years	12
provide valuable	12
ribosomal frameshifting	12
simulation time	12
dynamics calculations	12
model compounds	12
relationship studies	12
coding rnas	12
visible light	12
action potentials	12
contact structures	12
cambridge structural	12
dihedral angle	12
factor receptor	12
lipid monolayers	12
band structure	12
peptide hybrids	12
host phylogeny	12
threading algorithms	12
releasing hormone	12
reversed phase	12
plant defensins	12
peptides based	12
different lengths	12
residue peptide	12
deuterium exchange	12
methyl groups	12
dynamical properties	12
two approaches	12
stable complexes	12
known rna	12
protein crystallography	12
bodily fluids	12
rnase ii	12
membrane systems	12
structure using	12
evolutionarily related	12
potential targets	12
recently described	12
two subunits	12
activity towards	12
preliminary data	12
ribosomal protein	12
target structure	12
supplementary table	12
pro residue	12
folded structure	12
one protein	12
increasing interest	12
aromatic amino	12
strand rna	12
studies show	12
photosynthetic apparatus	12
structural study	12
plant species	12
previously published	12
modified peptides	12
statistical analysis	12
carbon atoms	12
peptide corresponding	12
disorder transitions	12
made possible	12
mainly due	12
crystallographic structure	12
bactericidal activity	12
amphiphilic peptides	12
two new	12
prediction algorithms	12
polyglutamic acid	12
cardiovascular disease	12
mother cell	12
loop structure	12
simplex virus	12
special interest	12
genetic material	12
charge transfer	12
widely distributed	12
ef ciency	12
frequently used	12
exchange chromatography	12
help us	12
theoretical studies	12
biological evaluation	12
max planck	12
long range	12
molecular replacement	12
related protein	12
conserved cysteine	12
method based	12
catalytic triad	12
conformational state	12
macromolecular structure	12
therapeutic targets	12
disordered residues	12
unfolded protein	12
tertiary pairs	12
tumor targeting	12
coding sequence	12
spectroscopic methods	12
new possibilities	12
highly effective	12
phospholipid bilayer	12
synthetic strategy	12
refractive index	12
fusion proteins	12
structural characteristics	12
molecular evolution	12
protein recognition	12
interaction networks	12
various cellular	12
moonlighting proteins	12
amyloid aggregates	12
structure alignments	12
structural details	12
various cell	12
spectroscopic analysis	12
high spatial	12
alignment methods	12
linear regression	12
bit vectors	12
accurately reproduced	12
molecular simulations	12
organic chemistry	12
helix formation	12
electron cryo	12
molecular details	12
acid analysis	12
small rnas	12
peptide complexes	12
two structures	12
melting temperature	12
high accuracy	12
lateral resolution	12
associated protein	12
resistance mechanisms	12
publicly available	12
rigid body	12
using surface	12
spatial scales	12
immune cells	12
different sequences	12
based assay	12
membrane environment	12
normal modes	12
two protein	11
one single	11
computational biology	11
resolution structural	11
functional residues	11
analysis tools	11
significantly increased	11
atom force	11
functional analysis	11
membered ring	11
virus replication	11
novel class	11
correct structural	11
substrate recognition	11
em reconstruction	11
previous results	11
like domains	11
strongly depends	11
interactions among	11
conformational search	11
af nity	11
binding constant	11
quantum yield	11
computational approach	11
spatial structure	11
docking study	11
specific sites	11
peptide drugs	11
rna fragment	11
plant peptides	11
coupling reagent	11
folding problem	11
candidate molecules	11
may affect	11
oxidative damage	11
additional information	11
virus rna	11
ph range	11
structure may	11
antimicrobial agents	11
good model	11
melanoma cells	11
generated using	11
force generation	11
spatial scale	11
entire sequence	11
structure data	11
assay using	11
unique structural	11
known inhibitors	11
biological relevance	11
reaction rate	11
capillary electrophoresis	11
relationships among	11
mass spectrometric	11
mitochondrial membrane	11
structure solution	11
protein regions	11
effi cacy	11
macromolecular crowding	11
atomic model	11
new approaches	11
lag phase	11
large proteins	11
using solid	11
magnetic force	11
electrostatic forces	11
molten globules	11
particularly important	11
coronavirus disease	11
waals interactions	11
materials science	11
em data	11
amadori products	11
phase transitions	11
recently identified	11
ex vivo	11
bond donor	11
rna tertiary	11
distance restraints	11
based modelling	11
data collected	11
pathological conditions	11
various protein	11
structural aspects	11
viral genomes	11
tyrosine residues	11
directly related	11
encapsidation signal	11
fold assignment	11
structure determinations	11
molecular target	11
laser beam	11
will lead	11
function paradigm	11
structural feature	11
ed peptides	11
lateral diffusion	11
rich sequence	11
polar interactions	11
computer algorithms	11
different sizes	11
bioactive molecules	11
surface tension	11
best results	11
recently shown	11
protein will	11
kinetic folding	11
dna gyrase	11
scanning tunneling	11
snow crystals	11
light microscope	11
cultured cells	11
steric clashes	11
genetic algorithm	11
tetrafl uoroborates	11
cleavage site	11
fl uorinated	11
viral protein	11
molecular design	11
planar lipid	11
human tumors	11
fundamental role	11
functional activity	11
folded states	11
acid type	11
compounds containing	11
membrane disruption	11
another example	11
provide evidence	11
solvent exposed	11
site directed	11
human beta	11
molecular targets	11
trans isomerization	11
interactions may	11
remains unknown	11
biochemical studies	11
functional significance	11
mer peptide	11
helical coiled	11
highly charged	11
culture medium	11
electron cryomicroscopy	11
important factor	11
gene transcription	11
di biofisica	11
new york	11
findings suggest	11
bacterial cells	11
vivo experiments	11
amyloid fi	11
peptides showed	11
deletion mutants	11
disordered sequences	11
living cell	11
different classes	11
acid substitutions	11
spectroscopic studies	11
native sequence	11
stem loops	11
expression levels	11
test set	11
fold increase	11
growth hormone	11
signi cantly	11
human brain	11
transmembrane helix	11
different molecular	11
carbon atom	11
reaction times	11
tobacco mosaic	11
membrane properties	11
flexible regions	11
based drugs	11
diagram graph	11
target receptor	11
important biological	11
second part	11
two classes	11
cellular components	11
terminal segment	11
million people	11
supplementary material	11
charged side	11
molecular model	11
structural insights	11
sarcoplasmic reticulum	11
nmr chemical	11
rate limiting	11
energy loss	11
important implications	11
using multiple	11
cys residue	11
ms analysis	11
structural fold	11
thermodynamic properties	11
closed state	11
endothelial growth	11
mm tris	11
molecular graphics	11
computational models	11
protein association	11
dimensional nmr	11
transport properties	11
enzyme catalysis	11
stimulated emission	11
relatively low	11
rate constant	11
using standard	11
residual dipolar	11
nicotinic acetylcholine	11
new model	11
two major	11
gel phase	11
docking simulations	11
protein modeling	11
cluster analysis	11
biological fluids	11
including pseudoknots	11
backscattered electron	11
bilayer membranes	11
rgd sequence	11
biological data	11
novel antimicrobial	11
structures deposited	11
zeta potential	11
significant decrease	11
functional relationships	11
assisted solid	11
thermofisher scientific	11
dynamic behavior	11
fluorescent probe	11
highly structured	11
pdb structures	11
virus glycoprotein	11
selective inhibitors	11
intracellular delivery	11
pharmacological properties	11
purified using	11
anticancer agents	11
molecular models	11
studies using	11
based molecular	11
solid supported	11
recombinant human	11
peptides will	11
western blot	11
different folds	11
fatty acyl	11
processes including	11
recent results	11
salt bridge	11
novel human	11
receptor antagonist	11
structure comparison	11
sequences seq	11
closed conformation	11
dichroism spectroscopy	11
genetic diseases	11
alternative approach	11
pdb files	11
will become	11
fl exible	11
large protein	11
changes induced	11
transfer function	11
atomic number	11
three peptides	11
molecular self	11
significant differences	11
main goal	11
antibody recognition	11
gnrh analogues	11
biochemical properties	11
murine leukemia	11
histocompatibility complex	11
detailed understanding	11
tof mass	11
amyloidogenic proteins	11
ion exchange	11
medical research	11
soluble oligomers	11
pair dataset	11
cell surfaces	11
data mining	11
efflux pumps	11
atomic models	11
fl exibility	11
host system	11
polyacrylamide gel	11
interactions using	11
highly ordered	11
structural environment	11
different secondary	11
chiral centers	11
given protein	11
blood cell	11
side reactions	11
associated proteins	11
among many	10
respiratory disease	10
virus spike	10
yeast cells	10
swelling power	10
sequence comparison	10
carbonyl groups	10
rst step	10
rna processing	10
structure changes	10
cancer patients	10
hepatitis virus	10
biomolecular chemistry	10
studying protein	10
potential anti	10
provide information	10
aggregation propensity	10
high sensitivity	10
different time	10
atp hydrolysis	10
membrane model	10
specifically bind	10
practical applications	10
interaction partners	10
different peptides	10
higher order	10
divalent ions	10
single cell	10
optical imaging	10
biological rnas	10
molecular oxygen	10
energy value	10
another approach	10
protein may	10
banana lectin	10
dynamic structure	10
identify new	10
protein residues	10
chemical information	10
brain tumors	10
alternative stem	10
biomolecular interactions	10
screening approach	10
computer science	10
natural peptides	10
clinical use	10
three proteins	10
lead compound	10
pharmacological activity	10
energy parameters	10
structural alignments	10
query segment	10
calcium ions	10
different approaches	10
concentration range	10
type pseudoknot	10
bound form	10
rna segments	10
interactions within	10
glycan structure	10
quantum mechanical	10
solution nmr	10
using chemical	10
anticancer activity	10
also reported	10