Index
Baell, 10.4.9
Chemical Label, 6.8.11
Beep, 4.20.11
Interaction Diagram, 16.3.7
Beta-Catenin, 16.21
bioisostere, 10.9.1
Bioactive Conformation, 16.21
chemical label, 6.8.11
Blast, 22.2.25
from PDB, 10.1.1
BlastDB Directory, 4.20.2
interaction diagram, 10.6
alphas, 6.8.3
screening, 15
C-alpha backbone, 5.5.11
C2′-endo pucker, 5.5.12
depiction, 10.20.2
C3′-endo pucker, 5.5.12
CHEMRIYA, 13.5
COLLADA, 3.6.1.7
CPK, 3.7.1
interactive ligand editor, 3.7.5
ligand editor, 16.3.4
Chemical Cluster, 21.6.3
object, 6.3.9
Search, 21.6.2
CisTransAmide Angle, 13.1.9.4
print, 6.7
Clash Threshold, 4.20.10
printing, 6.7
Computational Chemistry, 16.21
screening, 15
Computer-Aided Drug Discovery (CADD), 16.21
stereo, 6.6
Covalent Geometry., 16.21
visualization, 5.5.11
DILI, 10.11.5
3DMOLT, 18.5
3DQsar, 11.4
Decomposition, 10.36.3
3D_Similarity_PDB_Search, 5.7
Design Evolution, 12.10
3Dqsar tutorial, 21.14
Dimer, 5.5.11
bioisostere, 10.9.2
Display, 22.2.26
predict, 5.6
Distance, 13.1.9.4
helices strands, 5.6.1
Dock Directory, 4.20.2
local flexibility, 5.6.5
Docking, 22.2.26
protein health, 5.6.4
Drug Bank, 4.16.7
tools identify ligand binding pocket, 5.6.7
Design, 16.21
oda, 5.6.6
Editor, 4.20.2
Eintl, 12.1.10
dock, 16.15
Error in saving configuration settings: You are not a license administrator, 22.1.10
docking, 4.16.1
Extended Amino Acids, 16.21
64, 22.1.3
FILTER.Z, 4.20.2
A-form RNA, 5.5.12
gz, 4.20.2
AI, 12.10
uue, 4.20.2
FTP.createFile, 4.20.11
template, 10.37.3
keep File, 4.20.11
Acetyl Cap, 16.21
proxy, 4.20.11
ActiveICM, 3.6.1.12
Filter.zip, 4.20.2
Alignment mode, 5.5.11
Flexible Minimization, 16.21
Alpha-Helix Stabilization, 16.21
Force Auto Bond Typing, 4.20.11
Altona-Sundaralingam pseudorotation, 5.5.12
Free Wilson, 10.36.2
Atom Single Style, 4.20.3
Frequently Asked Questions, 22
GAMESS, 9.21.16
GPCR Modeling Example, 21.5.1
site Label Drag, 4.20.7
GRAPHIC.store Display, 4.20.3
Shift, 4.20.7
NtoC Rainbow, 4.20.4
siteArrow, 4.20.7
alignment Rainbow, 4.20.4
stereoMode, 4.20.3
atomLabelShift, 4.20.7
stickRadius, 4.20.1
ballStickRatio, 4.20.1
surfaceDotDensity, 4.20.3
center Follows Clipping, 4.20.3
surfaceDotSize, 4.20.3
clash Style, 4.20.3
surfaceProbeRadius, 4.20.3
clashWidth, 4.20.3
transparency, 4.20.3
clip Grobs, 4.20.3
wire Width, 4.20.1
Skin, 4.20.3
wormRadius, 4.20.9
Static, 4.20.3
xstick Backbone Ratio, 4.20.1
discrete Rainbow, 4.20.4
Hydrogen Ratio, 4.20.1
displayLineLabels, 4.20.7
Style, 4.20.1
displayMapBox, 4.20.3
Vw Ratio, 4.20.1
distance Label Drag, 4.20.1
GROB.arrowRadius, 4.20.3
dnaBallRadius, 4.20.9
atomSphereRadius, 4.20.3
dnaRibbonRatio, 4.20.9
contourSigmaIncrement, 4.20.3
dnaRibbonWidth, 4.20.9
relArrow Size, 4.20.3
dnaRibbonWorm, 4.20.9
relArrowHead, 4.20.3
dnaStickRadius, 4.20.9
GUI.auto Save, 4.20.4
dnaWormRadius, 4.20.9
Interval, 4.20.4
font Scale, 4.20.7
autoSave, 22.2.33
fontColor, 4.20.7
autoSaveInterval, 22.2.33
fontLineSpacing, 4.20.7
enumeration Memory Limit, 4.20.11
grobLineWidth, 4.20.3
max Nof Recent Files, 4.20.11
hbond Ball Period, 4.20.1
Sequence Length, 4.20.4
Style, 4.20.1
splash Screen Delay, 4.20.11
hbondAngleSharpness, 4.20.1
Image, 4.20.11
hbondMinStrength, 4.20.1
table Row Mark Colors, 4.20.4
hbondStyle, 4.20.1
workspace Folder Style, 4.20.4
hbondWidth, 4.20.1
workspaceTabStyle, 4.20.4
hetatmZoom, 4.20.1
GigaScreen, 18.5
hydrogenDisplay, 4.20.1
light, 4.20.3
lightPosition, 4.20.3
HTTP.proxy, 4.20.11
mapLineWidth, 4.20.3
support Cookies, 4.20.11
occupancy Radius Ratio, 4.20.3
user Agent, 4.20.11
occupancyDisplay, 4.20.3
Hbond to selection, 13.1.9.4
quality, 4.20.3
Hbonds, 16.3.4
rainbow Bar Style, 4.20.4
Helicon Peptide, 16.21
resLabelDrag, 4.20.7
Homodimer, 5.5.11
resize Keep Scale, 4.20.3
Homologous chains, 5.5.11
ribbonRatio, 4.20.9
To Guide, 3
ribbonWidth, 4.20.9
Html, 4.2.7
ribbonWorm, 4.20.9
Http Read Style, 4.20.11
rocking, 4.20.4
Hydrocarbon Staples, 16.21
Range, 4.20.4
Hydrogen.bond, 4.20.5
Speed, 4.20.4
I+4 Staple Position, 16.21
selectionStyle, 4.20.3
Staple Position, 16.21
Pro How To, 3.2
Mac, 22.1.15
analysis tools, 5.5.12
Atom Margin, 4.20.10
graphics crash, 22.1.11
Sigma Level, 4.20.10
object, 5.6.2
Markush, 21.6.9
start, 1
create, 21.6.7
ICM-Pro Tutorial, 16.21
File Size Mb, 4.20.11
IMAGE.bondLength2D, 4.20.6
Max_Fused_Rings, 10.11
color, 4.20.6
Mnconf, 4.20.10
compress, 4.20.6
Model, 11.4
gammaCorrection, 4.20.6
MolCart, 22.9
generateAlpha, 4.20.6
lineWidth, 4.20.6
lineWidth2D, 4.20.6
orientation, 4.20.6
MolPSA, 10.11
paper Size, 4.20.6
MolScreen, 15
previewResolution, 4.20.6
MolSoft ICM-Pro, 16.21
previewer, 4.20.6
MolVol, 10.11
print, 4.20.6
Molcart, 10.5.3
printerDPI, 4.20.6
scale, 4.20.6
Molecular Docking, 16.21
stereoAngle, 4.20.6
Dynamics, 14.5
stereoBase, 4.20.6
Preparation, 16.21
stereoText, 4.20.6
Movie.fade Nof Frames, 4.20.4
INCHI, 10.20.3
quality, 4.20.4
IQR, 17.4.6
Auto, 4.20.4
ISIS, 22.8.3
Multimer, 5.5.11
Icm Prompt, 4.20.10
NCBI, 22.2.25
NH2 Cap, 16.21
key, 10.3.20
NVIDIA, 22.1
Interaction Diagram 2D, 16.3.7
Natural Amino Acids, 16.21
Interactive Ligand Editor, 16.21
NephroTox, 10.11.4
Plot, 5.5.12
Nof_Atoms, 10.11
Internal Coordinates Table, 9.21.13
Nof_Chirals, 10.11
Directory, 4.20.2
Nof_HBA, 10.11
JPEG, 3.6.1.15
Nof_HBD, 10.11
KMZ, 3.6.1.7
Nof_Rings, 10.11
LCC, 13.5
Nof_RotBonds, 10.11
LigStrain, 16.21
Non-overlap, 13.1.9.4
Ligand Strain, 16.21
North conformation, 5.5.12
Liver Toxicity Models, 10.11.5
Nvidia GL failutre, 22.1.11
Log Directory, 4.20.2
ODA, 22.2.26
Optimal, 22.2.26
Output Directory, 4.20.2
Q and A, 14.5
chemicals, 10.4.9
MOL2, 13.1.3
analysis, 10.29
MOLT, 18.1
MOVIE.frame Grab Mode, 4.20.4
7UWI, 16.21
MPO, 10.34
Directory, 4.20.2
link, 17.1.40
RIDE, 18.5
RIDGE, 18.5
Field, 3.6.2.13
- Rapid Docking GPU Engine, 13.5
Homology, 3.6.2.15
Identity, 3.6.2.14
RMSF, 9.21.18
Sequence, 3.6.2.16
RNA, 4.17
convert, 5.1.2
backbone conformation, 5.5.12
PFAM, 3.6.1.7
chain analysis, 5.5.12
PLOT.Yratio, 4.20.8
conformation, 5.5.12
color, 4.20.8
pucker, 5.5.12
date, 4.20.8
structure analysis, 5.5.12
draw Tics, 4.20.8
sugar conformation, 5.5.12
font, 4.20.8
fontSize, 4.20.8
Score, 16.21
labelFont, 4.20.8
Ramachandran Plot, 5.5.9
lineWidth, 4.20.8
Real Format, 4.20.10
logo, 4.20.8
Reinforce Helix Tool, 16.21
markSize, 4.20.8
Relax Geometry Command, 16.21
orientation, 4.20.8
Label Shift, 4.20.7
paper Size, 4.20.8
Style, 4.20.7
previewer, 4.20.8
Residue Replacement, 16.21
rainbowStyle, 4.20.8
seriesLabels, 4.20.8
Rotation angle, 5.5.11
PLS, 11.1
Rotational symmetry axis, 5.5.11
PROPKA, 5.6.2
PROTAC, 12.14
PSA, 10.11.9
SCARE, 12.6.4
Peptide Engineering, 16.21
Mode, 16.21
Modeling, 16.21
SEQUENCE.site Colors, 4.20.4
Stapling, 16.21
SITE.label Style, 4.20.7
Pharmacophore RMSD, 13.1.9.4
labelOffset, 4.20.7
wrap Comment, 4.20.7
Projects Directory, 4.20.2
SLIDE.ignore Background Color, 4.20.4
Prosite Dat, 4.20.2
Fog, 4.20.4
Protein, 22.2.26
complex, 5.5.11
Protein-Peptide Interactions, 16.21
Select Min Grad, 4.20.10
Viewer, 4.20.2
Sequence Editing, 16.21
Pseudorotation Interactive Plot, 5.5.12
Show Res Code In Selection, 4.20.7
Pub Chem, 4.16.8
Sidechain Optimization, 16.21
PubMed Reference, 17.1.40
Pubchem, 4.16.8
South conformation, 5.5.12
Special Cases, 10.34.1.1
Strain, 12.4.3.1
and S, 22.5.21
Structural alignment, 5.5.11
R-Group, 10.36.3
Subunits, 5.5.11
R-groups, 16.5.3
SureChEMBL, 4.16.3
Swissprot, 3.6.1.7
link, 17.1.40
album, 6.15.3
Symmetry, 5.5.11
alias, 10.4.5
Temp Directory, 4.20.2
Terminal Capping, 16.21
color 2D scaffold, 10.14
Tools Analysis, 5.5.12
dna protein, 8.6.4
Torsion Minimization, 16.21
multiple, 8.6.5
Trimer, 5.5.11
sequence structure, 8.6.3
USER.email, 4.20.11
two sequences, 8.6.2
friends, 4.20.11
DNA to protein, 8.6.4
full Name, 4.20.11
organization, 4.20.11
phone, 4.20.11
alignment, 8.3.8, 8.6.1, 8.7.7, 8.7.7.1, 8.7.16, 8.8, 10.37.5, 10.37.6, 21.4.4, 22.4.12, 22.6, 22.6.2
Ultra Large Libraries, 18.5
annotation tutorial, 21.4.4
Uniprot, 17.1.40
box shade font, 8.7.7
VHL, 12.14
editing, 8.7.1
editor, 8.7
preferences, 13.1.4
example, 8.3.14
Van Drie, 10.36.5
font size, 22.2.1
Label Style, 4.20.7
format, 8.7.11
gaps, 8.7.11
Change, 13.1.9.4
image, 8.7.2
Water Radius, 4.20.10
profile, 21.4.4
Wilson, 10.36.2
reorder, 8.3.12
Wire Style, 4.20.1
search, 8.7.12
XPDB Directory, 4.20.2
secondary, 21.4.4
Xstick, 3.7.1
a-bright, 3.7.2
selection, 8.7.13
about model, 11.1.3
strength, 8.3.8
profile, 8.3.8
view options, 8.7.10
activeICM, 7.8
color, 8.7.9
comment, 8.7.6
advanced, 7.14
background images, 7.15
cut, 8.3.11
control, 7.13
display title, 8.7.10
activeicmjs, 7.16
editor, 8.7
extract, 8.3.10
gaps, 8.7.11
tutorial, 21.6.11
horizontal scroll, 8.7.10
add database, 10.10.3
image, 8.7.2
new data, 10.3.7
to table, 16.5.7
options, 8.7.10
adding fragment, 10.4.8
rename, 8.7.10
in editor, 10.4.8
reorder, 8.3.12
adjust row height, 22.2.39
ruler, 8.7.10
administration, 10.10.5
save, 8.7.2
advanced alignment selection, 8.7.14
search, 8.7.12
ai, 16.18
decoration, 16.18
sequence offset, 8.7.10
alanine, 12.6.4
table, 8.7.10
applying prediction models, 11.2
allosteric, 5.6.7
alpha, 3.7.2
channel, 4.20.6
arrange, 4.14.1
alphaFold, 4.3
window, 4.14.1
alphafold, 4.3
graph, 22.2.8
ambient, 3.7.2
as2_graph, 4.6.5
amidinium, 10.15
as_graph, 22.2.8
amino acid, 4.17
asparagine, 9.21.2
acids, 10.4.6
assign, 6.1.3
2D coordinates, 10.20.2
stereo faq, 22.1.8
helices, 5.6.1
strands, 5.6.1
angstrom, 22.4.7
charge, 22.4.21
atomLabelStyle, 4.20.7
view, 6.10.7
atomic energy circles, 16.3.5
store, 6.10.7.4
score, 10.38.2
animations, 7
alignment, 8.7.6
point, 10.35.4
by substructure, 10.13
author, 4.2.4
plot, 17.4.24
close tree, 10.28.5
annotation, 8.7.6
play slide, 7.13
autofit, 12.11
lines, 3.6.3.17
autosave, 22.2.33
lines, 3.6.3.17
available properties, 10.11.1
apf, 5.4.6, 5.8, 10.37.5, 10.37.6, 10.38, 11, 12.7, 13, 13.1.9.5, 13.3, 13.4, 16.3.11, 16.17, 21.8, 21.8.1, 21.8.2, 21.8.3, 21.8.4, 21.8.5, 22.8.12
ave, 17.7.1
flexible template, 10.37.6
pairwise, 10.37.5
axes, 17.4.15
super, 10.37.3
axis, 17.4.11
template, 16.12.3
options, 17.4.10
tools, 10.38
grid, 17.4.10
3DQSAR, 10.38.4
range, 17.4.10
consensus ph4, 10.38.1
title, 17.4.10
pairwise score, 10.38.2
screen, 10.38.3
coloring scale, 22.2.38
tutorial, 21.8
cluster, 21.8.5
consensus, 21.8.2
color shortcut, 22.2.2
score, 21.8.3
images activeicm, 7.15
screen, 21.8.4
image, 6.4.3
superposition, 21.8.1
backup, 3.6.2.11
alignment, 10.37.7
bad, 10.11
apf3Dqsa, 22.8.12
groups, 10.4.9
apo, 13.1.10
ball, 4.20.5
append, 17.1.44
and stick, 3.7.1
table, 17.1.44
balloon, 17.4.26
rows, 3.6.10.7
bases, 10.4.6
bye, 3.6.1.19
file, 12.3.2.2
alpha, 6.1.10
index, 12.3.2.4
trace, 6.1.10
loaded icm object, 12.3.2.1
ca-trace, 6.1.10
mol mol2, 12.3.2.3
cache, 7.14.1
molcart, 12.3.2.5
run, 12.3.3
properties, 10.11
bayesian classifier, 11
sequence similarity, 8.7.15
bbb, 10.11.6
startup, 22.10.2
beep, 22.2.35
begin docking simulation, 12.3
carboxylic acid, 10.15
best, 10.3.34
cartesian, 10.23
bicyclics, 10.4.6
cation, 5.2.5
cavities, 5.5
properties, 6.3.1
closed, 5.5.4
bioinfo align multiple, 8.3.7
two sequences, 8.3.5
cell, 5.3.2
links, 8.3.9
menu, 3.6.4
on ligand, 16.3.13
secondary structure, 8.3.2
and representative members, 17.7.2
translation, 8.3.3
cereblon, 12.14
bioisoester, 10.9
chain.breaks, 22.2.34
chair, 22.5.20
biological, 5.3.3
change box size, 16.9.1
height of all rows, 17.1.7
bit, 22.1.3
ligand, 16.5.1
residue number, 9.2
search, 4.16.4
row height, 17.1.7
blood brain barrier, 10.11.6
selection, 4.6.7
blue lines, 8.2
speed range, 6.10.7.2
boat, 22.5.20
changing font in alignment editor, 8.7
boltz, 4.3
charge, 3.6.3.21, 5.1.3, 5.1.3.1, 5.1.3.2, 6.8.2, 10.4.3, 10.5.1, 10.7.1, 10.7.2, 10.7.3, 10.38.1, 13.1.9.4, 22.4.1
covalent, 22.4.2
check box, 7.6.6
convert, 22.8.5
bonding, 6.1.8
export excel, 10.2.3
preferences, 4.20.1
save, 10.2
3D, 10.2.5
alignment, 21.4.4
editor, 10.2.4
size, 16.9.1
image, 10.2.6
table, 10.2.2
mode, 10.3.31
super, 10.37
molt, 18.2
view, 10.3.28
stack, 9.21.15
build, 6.10.7.1
chemical, 10, 10.3.28, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.4.10, 10.8, 10.10.4, 10.11.3, 10.20.2, 10.24, 10.35.4, 10.35.5, 10.37, 10.37.5, 10.37.6, 17.7.1, 21.6.4, 22.8.4, 22.8.5, 22.8.7, 22.8.8, 22.8.9, 22.8.10
2D qsar, 11.1.2
homology model, 9.1.2
descriptors, 22.8.15
hydrogens, 9.21.5
buried molSurface, 13.1.9.4
draw, 21.6.1
buttons, 7.14
spreadsheet tutorial, 21.6.1
convert, 10.20
not starting, 22.1.13
2dto3d, 10.20.1
fingerprint, 15
pca, 10.29
fingerprints, 22.8.15
smiles, 10.20.3
fragments, 10.3.33
duplicates, 10.33
group, 10.4.5
remove.redundant, 10.33
chemlib.so, 22.1.3
modifiers, 10.35.2
chemspace, 10.5.5
properties, 21.6.4
append, 21.6.4.4
right click, 10.4.3
build visualize, 21.6.4.1
compare, 21.6.4.8
filter, 10.5.2
delete row, 21.6.4.3
text, 10.5.4
distinguish, 21.6.4.7
sketch, 21.6.1
export, 21.6.4.5
space, 10.30
project, 21.6.4.6
select, 21.6.4.2
compare, 10.3.22
template, 10.3.2
chimeric ligands, 12.9
spreadsheets, 10.3
substituent, 10.9
substructure, 4.2.2
considerations, 12.1.3
chrome, 22.3
display, 10.3.3
cis trans proline, 21.5.2
tables, 17.2
toxicity, 10.11.3
volumes, 13.1.11
2D, 10.7
classes, 10.3.28
3D, 10.7
classification model, 15.5
append, 10.4.13
clear display and planes, 3.6.3.2
selection, 4.6.6
planes, 3.6.3.2
display.fit, 22.8.13
draw, 10.4.1
duplicates, 10.3.21
clipping, 22.2.19
load, 10.1
planes, 6
merge, 10.32
tool, 6.13
new, 10.4.1
tools, 6.13
properties, 10.3.19
clone, 3.6.1.2
read, 10.1
downstream cluster, 10.28.5
project, 16.23
cavities, 5.6.7
structure, 10.4.13
stack, 9.21.18
representative.center, 10.28.2
cns, 10.34
tutorials, 21.6
background, 6.4.2
conformations, 22.9.8
by, 6.4
conformers, 10.23
alignment, 8.8
chemical, 10.3.35
object, 6.12.7
faq, 22.2.20
key, 22.2.38
scale, 22.2.38
pharmacophore, 10.38.1
surface by proximity, 6.3.3
selection, 6.3.4
molecule, 3.6.1.1
table, 10.3.27
object, 3.6.1.1
2D sketch, 10.5.6.5
surface, 6.3.2
distance, 6.8.10
mesh, 6.3.9.3
table, 10.3.27
coloring, 6.4.1
chemical, 10.3.24
2D 3D, 10.7
annotation, 17.1.41
3D molecular editor, 10.4.16
order, 17.1.29
from pdb, 5.1.3
plot, 17.4.6
local database, 3.6.1.6
row width, 17.1.22
statistics, 17.1.32
chem, 10.7.1
visibility order, 17.1.28
smiles to 2D, 22.8.11
color, 17.1.10
local.database, 3.6.1.6
hide, 10.3.8
show, 10.3.8
coordinates, 10.1.3
combinatorial chemistry, 10.35
library, 21.6.8
cell, 17.1.36
combine, 3.6.10.5
chemical, 10.3.25
display style, 4.20.9
loop, 9.5
command, 22.5.16
paste row, 17.1.35
line, 22.2.32
row, 17.1.36
commands, 22.10.1
rows, 17.1.44
common substructure, 10.37.1
selection to table, 17.1.37
compact tree, 10.28.5
chemical, 10.3.16
covalent, 16.10.1
table, 10.3.22
tables, 10.31
compatible, 3.6.1.10
tutorial, 21.9.3
crash, 3.6.2.11
compounds, 22.9.3
creat, 7.6.1
compress, 4.20.6
create, 17.1.1
compressed, 17.1.6
markush, 10.35.3
table view, 17.1.6
new objects, 4.17
conditions, 10.5.2
cross, 22.2.10
gen, 10.23
section, 6.13
configuration error, 22.1.19
cryptic, 5.6.7
crystal, 5.3.2
conformational entropy, 10.27
crystallographic analysis, 5.3
contour map, 5.3.6
selection, 3.6.2.1
convert2grid, 5.3.7
tether, 9.21.5
crystallographic cell, 5.3.2
dendrogram, 10.30.1
load eds, 5.3.4
denovo, 12.9
maps cell, 5.3.5
symmetry packing, 5.3.1
tools, 21.3.8
deselect, 22.2.7
cell, 3.6.5
neigbor, 5.3.1
deviation, 22.4.7
neighbors, 3.6.5
dfa, 15.3.3
dfz, 15.3.2
dialog, 7.6.5
current, 22.2.22
diffuse, 3.7.2
slide, 7.13
curves, 17.4.5
angle, 5.5
dimensional, 22.8.6
actions, 17.1.40
directories preferences, 4.20.2
fragments, 10.13
directory, 4.20
label, 6.8.8
disappearing labels, 22.1.12
rotation, 6.12.2
dislay ligand receptor interaction, 10.6
customized MPO score, 10.34.1
display, 4.5, 4.14.1, 4.20, 5.2.4, 5.2.4.1, 5.2.4.2, 6.8.15, 6.14, 10.25, 12.2.1.3.3, 22.2.4, 22.2.5, 22.2.8, 22.2.10, 22.2.11, 22.2.17, 22.2.21, 22.2.30, 22.2.32, 22.4.10, 22.4.11, 22.4.20, 22.8.4
cut, 17.1.35
chemical, 6.8.11
vertical alignment block, 8.3.11
delete distances, 6.9.4
cyclic peptide, 9.20
dihedral, 6.9.3
cys, 5.6.3
distance restraints, 6.8.14
cysteine reactivity, 5.6.3
distance2, 6.9.1
damaged skin, 22.1.12
angles, 6.9
dash, 22.2.12
formal charge, 6.1.9
gradient, 6.8.17
file format, 13.1.3
hbond, 13.1.9.3
search and alignment, 8.4
databases, 22.9.3
hydrogen, 6.1.7
novo, 12.10
atoms ligand editor, 16.3.3
design, 12.9
mesh, 6.3.5
decompose.library, 21.6.9
meshes, 6.3.8
options, 16.3
decoration, 16.18
planar angle, 6.9.2
default, 4.14
tether, 6.8.13
alignment, 8.7.5
toggle, 6.8.16
all, 3.6.2.2
CPK, 6.1.5
column row, 17.1.38
angle, 6.9.2
label, 6.8.9
chemical, 10.3.3
alignment, 8.7.5
dihedral.angle, 6.9.3
all, 3.6.2.2
angle.label, 6.9.4
electrostatic, 3.6.3.21
column, 17.1.38
energy.gradient, 6.8.17
distance.label, 6.9.4
hydrogen, 6.1.7
label, 6.8.9
polar, 6.1.7
row, 17.1.38
macroshape, 6.3.6
and display.macroshape, 3.7.6
template, 12.7
molecule, 10.3.24
templates, 16.12.3
origin, 6.8.12
tutorials, 21.9
potential, 3.6.3.21
waters, 12.1.8
representations, 3.7.1
background, 22.5.19
restraints, 6.8.14
batch, 12.3.2
ribbon, 6.1.3
conformations, 22.5.20
skin, 6.1.4
flexible.rings, 22.5.20
status, 22.2.32
hitlist, 12.4.3
interactive, 12.3.1
surfaces, 3.7.6
preparation, 12.2.1
table, 10.3.3
procedure, 12.3
tethers, 6.8.13
rank, 12.4.3
wire, 6.1.1
xstick, 6.1.2
sampling, 22.5.20
score, 12.4.3
faq, 22.4.10
stack, 12.4.2
restraint, 12.5
template, 12.7
label, 4.20.7
distances, 3.7.3
navigation, 7.6.7
documents, 6.15.3
bonds, 9.17
dollar, 22.10.3
diverse set, 17.7
donator, 10.4.9
dock, 12, 12.11, 16.10, 16.10.1, 21.9.3, 21.11.1, 21.11.2, 21.12.1, 22.5.3, 22.5.4, 22.5.5, 22.5.7, 22.5.8, 22.5.10, 22.5.11, 22.5.12, 22.5.13, 22.5.14, 22.5.15, 22.5.16, 22.5.21
envelope, 3.7.1
apf, 16.17
surface, 4.20.5
chemical table, 12.3.4
dotted line, 6.1.3
command, 22.5.16
lines, 22.2.34
macrocylce, 22.5.20
double, 10.4.10
start, 12.1
doublet, 10.4.7
table, 16.10
covalent, 16.10.1
dpc, 15.3.4
docked ligand strain, 12.1.10
docking, 5.6.6, 12, 12.1, 12.2, 12.2.1, 12.4.5, 12.6, 12.6.1, 12.6.2, 12.6.3, 12.13, 12.13.1, 12.13.2, 12.13.3, 12.13.4, 12.13.5, 12.13.6, 12.13.8, 12.13.9, 12.13.10, 13.1, 13.1.1, 13.1.2, 13.1.6, 13.2, 13.5, 16.10, 16.10.1, 16.11, 21.9, 21.9.1, 21.9.2, 21.11.3, 21.12, 21.12.2, 22.5, 22.5.1, 22.5.9, 22.5.17, 22.5.18
and drop sequences, 8.6.6
batch index, 12.3.2.4
residue label, 3.6.3.16
covalent, 12.8
draganddrop, 4.12
display, 12.4.6
explicit group, 21.12.2
chemical, 10.4.1
macrocycles, 12.2.1.3
preferences, 12.2.1.3
like, 10.11.6
database scan, 12.2.1.3.2
drugbank, 10.1
display, 12.2.1.3.3
druglikeness, 10.4.9
general, 12.2.1.3.1
dsPocket, 4.9
project, 13.1.5
dual alanine scanning, 12.6.4
table, 13.1.5
easy rotate, 3.6.3.12
results display, 12.4.6
ecfp, 11.3
setup, 22.5.13
start, 12.2.1
2D, 16.5.1
steps, 12.2
add sequence, 10.4.17
chemical moledit, 10.3.26
endocyclic torsion angles, 5.5.12
2D, 16.5.1
circles, 13.1.11
editor preferences, 16.2
multiple substituents, 16.5.2
terms, 9.21.19
tools, 3.6.2.17
ensemble, 12.6.2
menu, 3.6.2
calculations, 9.21.18
molecular document, 7.6.1
molecule, 10.4
enumerate formal charge states, 10.18
molt, 18.3
reaction, 21.6.10
selection, 3.6.2.5
enumeration, 10.35.4
slide, 7.4.1
eps, 10.2.6
table row, 17.1.24
epsilon, 22.4.15
molecule, 10.3.26
eraser, 10.4.11
structure, 10.3.26
errno, 22.1.3
editor, 22.4.12
editpdbsearch, 3.6.2.12
evaluate score strain, 16.4
exact, 10.31
excel, 10.2.3
on binding tutorial, 21.5.3
exclude fragment, 10.5.2
example2, 21.5.3.1
volume, 16.3.11
stability tutorial, 21.5.4
exit, 3.6.1.19
point, 16.19
denisty map, 5.3.5
flex, 12.6.1
group, 12.6.3
contour, 3.6.5
docking, 12.6.3
electrostatic coloring scale, 22.2.38
groups, 21.12.2
potential, 3.6.3.21
surface, 6.3
dock project, 16.22
pdb, 4.19
elegant sketch, 6.10.4
extra windows, 6.2
element, 10.4.10
eln, 19.7
2D, 10.1.1
embed browser, 7.11
3d coordinates to spreadsheet, 10.1.3
powerpoint03, 7.8
icb, 3.6.1.5
powerpoint07, 7.9
object icb, 4.18.2
powerpoint10, 7.10
sub alignment, 8.3.10
activeicm, 7.13
icb, 3.6.1.5
script, 7.13
pharmacophore, 10.5.6.4
ISISdraw, 22.8.3
MolCart, 22.9
microsoft, 7.7
activeicm, 22.3
path, 22.3.3
empty hostid, 22.1.18
alignment secondary structure, 22.6.2
enamine, 10.5.5
apf model, 22.8.12
real, 13.5
atom charge, 22.4.21
enantiomer, 22.5.21
display, 22.2.17
enantiomers, 12.1.3
autosave, 22.2.33
background color, 22.2.2
measure distance ring, 22.8.16
job, 22.5.19
merge, 22.4.5
beep, 22.2.35
modeling, 22.7
binding energy, 22.5.2
molcart 64bit, 22.1.3
blend transition, 22.2.31
query, 22.9.5
breaks, 22.2.34
sdf, 22.9.4
change torsion, 22.4.16
text search, 22.9.6
chem table display, 22.8.4
molecule c, 22.2.5
chemical monitor, 22.8.10
moledit, 22.8.2
query2, 22.8.1
movie planes, 22.2.19
cheminformatics, 22.8
newscript, 22.10.1
clipping plane, 22.2.11
nmr, 22.4.18
closest, 22.4.22
nvidia error, 22.1.2
color carbon, 22.2.4
origin, 22.2.10
skin, 22.2.16
plist, 22.1.9
command line display, 22.2.32
pmf score, 22.5.6
convert chemical from pdb, 22.4.1
pockets, 22.2.14
covalent bond, 22.4.2
preserve coordinates, 22.8.6
delete, 22.4.9
quad buffer, 22.1.7
descriptors, 22.8.15
receptor selection, 22.5.14
deselect, 22.2.7
reload dock, 22.5.4
dihedral, 22.2.18
remove salt, 22.8.14
dock charge groups, 22.5.22
select, 22.2.6
probe, 22.5.13
renumber, 22.4.4
racemic, 22.5.21
residue number selection, 22.2.36
repeat, 22.5.5
rmsd, 22.4.7
working directory, 22.5.23
rmsdtips, 22.4.8
docking, 22.5
rocking active ppt, 22.3.1
docktime, 22.5.11
speed, 22.3.2
dollar, 22.10.3
rotate chemical, 22.8.13
download install, 22.1.1
scale display, 22.2.38
druglikeness, 22.8.9
scanScoreExternal, 22.5.17
energy, 22.5.1
scanScoreExternal2, 22.5.18
error admin, 22.1.10
score, 22.5.8
extract ligand, 22.8.8
script, 22.10
flexible dock, 22.5.15
sequence secondary structure, 22.6.1
ring docking, 22.5.20
alignments, 22.6
font size, 22.2.1
smiles, 22.8.11
foreground table, 22.10.4
solvent accessible surface table, 22.4.19
gl failure, 22.1.11
ss, 22.4.17
gui, 22.2
structure, 22.4
guided dock, 22.5.3
superimpose, 22.4.6
hitlist, 22.5.7
surface display, 22.2.37
hydrogen bond acceptors, 22.8.17
thoroughness, 22.5.12
iSee, 22.2.30
transparent ribbon, 22.2.3
icmPocketFinder, 22.5.10
truncate mesh, 22.2.15
insert column, 22.8.7
view stack, 22.9.8
installation, 22.1
weak hydrogen bonds, 22.4.20
interactions, 22.2.12
write pdb, 22.4.3
ligandbox, 22.5.9
faqcontour, 22.2.28
faqmaps, 22.2.27
fragments, 10.8
faqoda, 22.2.26
frame, 8.3.3
faqstereo, 22.1.14
fasta, 8.1.5
radical, 10.4.7
fbdd, 13.2
wilson regression analysis, 10.36.2
fft, 12.13.1
freedomspace, 10.5.5
protein protein docking, 12.13.1
freeze column, 17.1.30
file, 3.6.1.3
row, 17.1.31
close, 3.6.1.13
frequency, 10.3.35
compatible, 3.6.1.10
export, 3.6.1.12
full model, 9.1.3
high quality image, 6.15.1
builder, 9.1.3
load, 3.6.1.7
multiple chain, 9.1.3.1
menu, 3.6.1
refinement, 9.1.3
password, 3.6.1.11
scene antialias, 3.6.3.10
preferences, 3.6.1.16
screen, 3.6.3.8
quick image, 3.6.1.14
icb, 4.11
functional.groups, 10.13
recent, 3.6.1.17
furanose ring conformation, 5.5.12
bak, 3.6.2.11
fuzzy, 12.7
gap, 9.4
selection, 4.6.8
general preferences, 4.20.5
filters, 13.1.5
generalselecttools, 4.6.1
find chemical, 10.3.32
getting started, 4
method, 11.3
giga search, 10.5.5
fingerprints, 22.8.15
sized library, 13.5
firefox, 22.3
gigasearch, 10.5.5
ginger, 10.23
five-membered ring conformation, 5.5.12
glutamine proline, 9.21.2
google, 3.6.1.7
objects, 6.3.7
APF superposition to template, 10.37.4
docking, 16.13
gpcr_model, 21.5.1
receptor groups, 16.13
graft loop, 9.5
ring sampling level, 12.2.1.3
graphical, 22.2.4
flood, 9.21.17
tutorial, 21.1
2D3D labels, 21.1.4
preferences, 4.20.7
annotation, 21.1.2
color representation, 21.1.1
form view, 17.1.5
labels, 21.1.3
user interface, 22.2
card, 22.1.2
controls, 6
defects, 22.1.12
effects, 6.10
linking, 16.11
panel, 6.2
screening, 13.2
preferences, 4.20.3
cluster apf, 13.1.9.5
columns, 12.4.3.1
export, 12.4.4
column, 17.1.46
groupGen, 16.18
introduction, 9.1.1
older versions, 9.1.1.3
guanidinium, 10.15
hover, 17.4.26
3D editor, 21.7
menus, 3.6
add columns, 10.3.4
preferences, 4.20.4
cluster center, 10.28.2
tabs, 3.7
color 2D by ph4, 10.5.6.5
copy 2D, 10.3.16
paste, 10.3.6
halogen, 10.11.2
decompose, 21.6.9
duplicate chemicals, 10.3.21
hba, 13.1.10
edit table, 10.3.17
hbd, 13.1.10
tree, 10.28.4
excel, 10.3.10
strength, 22.2.29
extract 3D ph4, 10.5.6.4
filter, 10.3.12
health, 5.6.4
find replace, 10.3.13
heatmap, 17.4.7
mark row, 10.3.14
example, 17.4.7.1
markush, 21.6.8
helix, 22.2.20
structure, 21.6.7
help, 2
merge tables, 10.3.23
videos, 2
properties, 10.3.19
hetero, 10.3.28
reactions, 21.6.10
scan, 16.7
reorder, 10.28.3
hidden block format, 8.7.11
sdf, 10.3.9
width, 8.7.11
show hide, 10.3.8
hide, 17.1.39
sort column, 10.3.5
column, 17.1.28
standardize, 10.3.18
high, 3.6.1.15
table hyperlinks, 10.3.15
quality, 3.6.3.11
print, 10.3.11
highlight new data, 10.3.7.1
activeicm, 3.3
his, 22.4.15
create molecular documents, 3.3.3
slides, 3.3.2
tautomer, 22.4.15
getting started, 3.3.1
histogram, 13.1.9.2, 17.4, 17.4.1, 17.4.9, 17.4.11, 17.4.13, 17.4.14, 17.4.15, 17.4.16, 17.4.17, 17.4.18, 17.4.20, 17.4.22
ppt, 3.3.4
bins, 17.4.3
web, 3.3.5
options, 17.4.2
chemical clusering, 10.28.1
bin.size, 17.4.2
icm browser convert display pocket, 3.1.4
bins, 17.4.3
distances angles, 3.1.9
color, 17.4.2
get started, 3.1.1
source, 17.4.2
graphical display, 3.1.2
style, 17.4.2
effects, 3.1.5
title, 17.4.2
images, 3.1.7
historeceptomics, 4.16.9
labels annotation, 3.1.6
get started, 3.2.1
graphics, 3.2.2
icmdb, 19
plots, 3.2.8
icmjs, 7.16
sequence analysis, 3.2.7
icmpocketfinder, 21.3.7
structure analysis, 3.2.3
id, 17.1.27
superimpose, 3.2.5
identity, 4.2.3
surfaces, 3.2.4
selections, 3.1.3
advanced, 6.15.3
superimpose, 3.1.8
distortion, 22.1.20
search, 4.16
preferences, 4.20.6
hrydrogen.bond, 22.2.29
problem, 22.1.20
multiple, 3.6.1.7
html-doc font size, 22.2.1
quality, 3.6.3.11
images, 6.15
atom display, 16.3.3
impose, 12.6.2
in-a-window, 22.1.7
acceptors, 22.8.17
inchi, 10.20.3
donor, 10.38.1
increment, 17.1.27
label edit, 5.2.4.1
id, 17.1.27
move, 5.2.4.2
index, 22.9.6
induced, 22.5.15
hydrogens, 10.3.28
insert, 7.6.4
remove, 10.3.18
column, 17.1.26
hyrophobic, 10.38.1
table, 17.1.34
row, 17.1.33
script, 7.6.4
icm, 22.3.3
chemist howto chemical search, 3.4.3
installation, 22.1
cluster, 3.4.5
combi library, 3.4.7
fingerprint, 13.1.9.6
ph4, 3.4.4
fingerprints, 13.1.9.6
plots, 3.4.8
lists, 13.1.10
sketch, 3.4.1
restraint, 12.5
spreadsheets, 3.4.2
restraints, 12.5
stereoisomers tautomers, 3.4.6
pro 3D ligand editor, 3.5.1
chem3D, 3.5.2
loaded ligand, 12.3.1.2
chemsuper, 3.5.4
loop, 9.1.4.2
energy, 3.5.3
modeling, 9.1.4
qsar, 3.5.5
table ligand, 12.3.1.1
tutorials, 3.5
modeling, 9.1.4
tutorials, 3.4
interface prediction, 21.10
hanging, 22.1.13
internal hydrogen bonds, 12.1.5
internet explorer, 22.3
script, 17.1.40
interrupt, 6.10.7.3
icm-crash, 22.1.13
animation, 6.10.7.3
icmFastAlignment, 8.4
introduction, 1
invisible residue label, 22.1.12
size, 22.1.9
iqr, 17.4.23
sdf, 10.1.2
isee, 7.6.5
layer, 6.14
isis, 10.4.18
layers, 6.14
isostere, 13.4
learning, 11
theory, 11.5
javascript, 7.16
least.squares, 17.4.16
job, 22.5.19
library, 10.35.4
join, 10.32
reaction, 21.6.10
jpg, 6.15
license, 22.1.4
means, 17.7.1
ligand, 5.2.3, 10.6, 10.27, 10.27.1, 10.27.2, 12.1, 12.6, 12.13.6, 12.13.7, 16.3.12, 16.3.13, 16.5.8, 16.10, 16.11, 22.4.5, 22.4.11, 22.5.2, 22.5.9, 22.8.8
aide, 12.10
keep carboxyls neutral, 12.2.1.3
kernel regression, 15.3.1
best replace, 16.6
chemical, 10.4.10
binding, 9.16
keyboard mouse, 6.11
keystokes in chem-edit, 10.4.10
considerations, 12.1.2
knime, 20
bioisostere, 16.8
covalent docking, 16.16
atoms, 6.8.2
mrc, 16.15
color, 6.8.7
preferences, 3.6.2.18
move, 6.8.4
energetics, 10.27
residues, 6.8.3
conformational entropy, 10.27.1
sites, 6.8.6
strain, 10.27.2
variables, 6.8.5
2D, 3.7.3
surface, 16.3.2
receptor contacts, 16.3.12
atom, 6.8.1
display, 5.2
atoms, 6.8.2
interaction, 10.6
color, 6.8.7
strain, 16.3.10
custom, 6.8.8
surface, 5.2.3
tether, 16.12
distance, 6.8.10
drag, 3.6.3.16
ligand-induced RNA conformational changes, 5.5.12
convert, 9.21.1
residue, 6.8.1
residues, 6.8.3
binding.re-dock ligand, 16.9
site, 6.8.1
display, 16.3
sites, 6.8.6
edit, 16.5
variable, 6.8.1
energy, 16.3
hydrogen.bond, 16.3
labeling, 6.8.1
pocket, 16.3
preferences, 16.2
distances, 6.8.10
restraint, 16.12
tab, 3.7.3
surface, 16.3
landscape, 4.20.6
tether, 16.12
large chemical space, 21.6.4
optimization, 21.11.3
font, 22.1.16
pocket, 4.9
ligand_pocket_interactions, 5.2.1
tutorial, 21.5.2
ligedit distance restraint, 16.12.2
tab, 3.7.5
preferred residues, 9.6
tether, 16.12.1
model, 9.21.9
light, 3.7.2
sample, 9.21.9
tab, 3.7.2
energy water, 9.21.17
font, 22.1.16
size, 22.1.16
lineWidth, 4.20.3
machine learning, 21.13
link, 8.3.9
macrocycles, 9.20
structure to alignment, 21.4
macros, 7.14
linker, 12.14
links, 4.6.20
linux, 10.10.1
alignment, 8.6.1
lipinski rule, 10.34
animation, 6.10.7.1
list, 4.6.18
apf docking sar model, 15.6
liver, 10.11.5
lmhostid, 22.1.18
flat, 22.8.13
molecular document, 7.6
example alignment, 8.3.14
molt, 18.1
nmr model, 4.2.5
receptor maps, 12.2.1.2
pdb hyperlinks, 4.2.6
selection, 4.6
protein structure, 5.1.1
level, 4.6.3
sequence, 8.1
bond, 22.4.2
extract pdb, 8.1.3
from file, 8.1.4
molecule, 3.6.1.1
paste, 8.1.2
object, 3.6.1.1
swissprot, 8.1.1
making molecular slides, 7.1
libraries, 9.21.6
html, 7.6
manual change torsion, 16.5.4
databases, 18
database.browse, 18.2
cel, 5.3.5
edit, 18.3
query, 18.4
mark, 17.1.45
row, 18.3
row, 17.1.45
localpdb, 22.2.24
color, 17.4.14
localseq, 22.2.25
shape, 17.4.13
size, 17.4.13
logD, 10.11.8
docking, 21.11.3
library, 21.6.8
mass, 22.4.22
logarithmic, 17.4.11
logout, 3.6.1.19
analysis, 10.36.6
materials, 3.7.6
analysis, 9.7
max, 17.7.1
design, 9.4
maxColorPotential, 4.20.10
find pdb segments, 9.7
dendrogram, 10.30.1
rgroup decomposition, 10.28.7
amino acid, 9.12
group, 9.11
measure distance, 22.8.16
to ring, 22.8.16
molcart, 10.10, 10.10.1, 10.10.2, 10.10.3, 10.10.4, 10.10.5, 18, 19, 22.1.3, 22.8, 22.8.1, 22.9.3, 22.9.4, 22.9.5, 22.9.6
add database, 10.10.3
exposed docking, 12.1.7
administration, 10.10.5
memory, 10.1.2
connect, 22.9.2
menu, 7.6.5
download dbs, 22.9.3
chemistry, 3.6.14
hostid, 22.9.1
docking, 3.6.15
installation, 10.10.1
homology, 3.6.13
license, 22.1.4
molmechanics, 3.6.16
search, 10.10.4
tools chemical search, 3.6.11
start, 10.10.2
molecular editor, 3.6.12
connect, 22.9.2
windows, 3.6.17
hostid, 22.9.1
license, 22.9.1
two sets, 10.32
molclart, 22.1.4
mesh, 5.2.2, 5.2.3, 5.3.4, 5.3.6, 5.3.7, 6.3, 6.3.9.1, 6.3.9.2, 6.3.9.4, 6.3.10, 6.3.11, 6.3.12, 6.13.1
clip, 6.3.10
animations slides, 7
color lighting, 6.3.9.4
documents, 21.2
options, 6.3.9
representation, 6.3.9.3
membrane, 14.3
save, 6.3.11
restraints, 14.2
options, 6.3.9
run, 14.1
vls, 14.4
surfaces grobs, 6.3
editor, 22.8.2
tab, 3.7.6
graphics, 6
metabolic oxidation, 15.7
matched pairs, 21.6.11
min, 17.7.1
mechanics, 9.21
minimization, 9.18
convert, 9.21.1
cartesian, 9.21.8
design loop, 9.21.10
global, 9.21.8
edit structure, 9.21.5
local, 9.21.8
gamess, 9.21.16
minimum specifications, 1
generate normal mode stack, 9.21.14
his asn, 9.21.2
type, 6.8.2
ic table, 9.21.13
mmp, 21.6.11
impose conformation, 9.21.4
mnSolutions, 4.20.10
minimize, 9.21.8
mmff, 9.21.6
domain interaction, 9.18
regularization, 9.21.3
start, 9.1.1.2
sample loop, 9.21.9
weight, 11.1.4
peptide, 9.21.12
modelers view, 9.1.4.1
protein, 9.21.11
view, 9.1.4.1
terms, 9.21.19
modeling, 9.21.3
view stack, 9.21.15
options, 9.1.1.1
modeling, 9
modeller view, 9.1.4
table, 10.20.2
modification history, 16.5.6
weight, 10.4.9
modify, 9.12
moledit, 10.4.8
position group scan, 16.7
molmechanics, 22.9.8
rec, 12.6.2
minimize, 9.21.8
mmff, 9.21.6
docking, 16.15
protein, 22.2.5
custom model panel, 15.4
load models, 15.1.1
run, 15.1
residue, 22.4.13
model type, 15.3
N C, 22.4.14
results, 15.2
molskin, 6.3.2
protein binding, 9.13
molsynth, 10.11.7
ligand, 9.16
peptide, 9.15
monitor, 22.8.10
stability, 9.14
monochrome, 10.3.28
mysql, 19
montecarlo, 22.9.7
navigate workspace, 4.6.10
nearest, 22.4.22
nephrotox, 10.11.4
column, 17.1.28
Torsion Profile Neural Network Prediction Engine, 6.12.6.1
mesh, 6.3.9.2
new, 8.1
slide, 7.4.2
icm session, 3.6.1.2
structure, 6.12
table, 17.1.1
tools, 6
table, 17.1.1
rotate, 6.11
nmr, 22.4.18
slab, 6.11
model, 4.2.5
translate, 6.11
nnc, 15.3.5
z-rotation, 6.11
nntorsion, 6.12.6.1
zoom, 6.11
nof, 10.11.2
chemical, 10.11.2
montecarlo, 22.9.7
non-contiguous selection, 4.6.18
normal modes, 9.21.14
nucleic acid conformation analysis, 5.5.12
mpa, 21.6.11
geometry, 5.5.12
nucleotide analysis, 5.5.12
conformation, 5.5.12
mpo, 10.34
geometry, 5.5.12
binary classification, 10.34.2
puckering, 5.5.12
custom step function, 10.34.1.2
number of sp3, 10.11.2
customized, 10.34.1
numbers, 10.3.28
save, 10.34.1.3
nvidia, 22.1.2
special cases, 10.34.1.1
obj, 6.7
mtl, 6.7
multi apf super, 10.37.7
objects, 5.1.2
panel, 6.2
in table, 17.3
parameter optimization, 10.34
in.table, 17.3
template, 9.1.4.3
windows, 6.2
shading, 6.3.12
effect, 6.10.5
older version, 3.6.1.10
online databases, 10.5.5
ph4, 10.5.6
draw 2d, 10.5.6.1
file, 4.18
3d, 10.5.6.2
password, 4.18.1
search, 10.5.6.3
with password, 3.6.1.4
2D, 21.6.6
3D, 21.6.5
clone, 10.5.6.2
optimize, 9.21.2
draw2D, 10.5.6.1
oracle, 19
draw3D, 10.5.6.2
orange, 4.6.5
selection, 4.6.5
move, 10.5.6.2
new, 10.5.6.2
orthosteric, 5.6.7
other selection, 4.6.19
phase angle P, 5.5.12
outside, 22.5.9
phylogenetic, 8.7.8
phylogeny, 8.7.8
pKa, 5.6.2
physics-based score, 12.4.3.1
package.activeicm, 7.13
pi, 5.2.5
packing, 5.3.1
cation, 5.2.5
pages, 19.7
pi, 5.2.5
picking, 6
apf score, 10.38
parallelization, 13.1.7
tips, 4.15
password, 10.10.5
chart, 17.4.8
pipi, 5.2.5
pca, 17.5
pka, 10.15
chem gl, 10.7.3
angle, 5.5
iw, 10.7.2
angle, 6.9.2
dormat, 4.19
file, 22.4.3
faq, 22.2.21
html, 4.2.7
plot, 4.20, 4.20.8, 13.1.9.2, 17.4, 17.4.1, 17.4.4, 17.4.9, 17.4.11, 17.4.13, 17.4.14, 17.4.15, 17.4.16, 17.4.17, 17.4.18, 17.4.20, 17.4.21, 17.4.22, 17.4.23
preparation, 21.3.11
R group sar, 10.36.4
axis, 17.4.11
hyperlinks, 4.2.6
color, 17.4.14
convert, 9.21.1
columns, 17.4.6
recent, 3.6.1.18
grid, 17.4.15
pdbsearchfield, 3.6.2.13
header, 17.4.9
pdbsearchhomology, 3.6.2.15
inline, 17.4.22
pdbsearchidentity, 3.6.2.14
logarithmic, 17.4.12
pdbsearcsequence, 3.6.2.16
mark, 17.4.13
mean median iqr, 17.4.23
docking, 12.12
point label, 17.4.19
modeling, 9.20
preferences, 4.20.8
editor, 16.21
groups, 17.4.25
selection, 17.4.18
components, 11.5
zoom translate, 17.4.17
axis, 17.4.15
alignment, 8.7.4
display, 17.4.15
plot, 17.4.20
grid, 17.4.15
alignment, 8.7.4
inline, 17.4.22
printer.resolution, 4.20.6
logarithmic, 17.4.12
pro-drug, 10.26
pmf, 22.5.6
problem, 22.1.14
with selection, 22.1.12
prodrug, 10.26
conservation, 22.4.12
properties, 5.8
close, 3.6.1.13
peptide, 4.9
rename, 3.6.1.9
properties, 4.9
pockets, 5.6.7
expression, 13.1.9.4
point label, 17.4.19
monitor, 10.4.9
portait, 4.20.6
protac, 12.14
post edit ligand, 16.5.8
protect, 7.6.8
screen, 13.1.9
postscript, 4.20.6
chain, 9.4
potential mean force, 13.1.4
health, 5.6.4
ppbatch, 12.13.9
model, 9.19
ppepitope, 12.13.7
protein docking, 21.10
ppmaps, 12.13.8
tutorial, 21.10
pprefine, 12.13.11
sculpting, 9.18
ppresults, 12.13.10
sequence, 10.4.17
pproc, 12.13.3
structure, 5
ppsetligand, 12.13.6
analysis, 5.5
ppsetproject, 12.13.4
closed cavities, 5.5.4
ppsetreceptor, 12.13.5
contact areas, 5.5.3
distance, 5.5.6
find related chains, 5.5.1
disulfide, 9.17
finding dihedral angle, 5.5.8
metabolic oxidation, 15.7
planar angle, 5.5.7
predicting bioassays, 11.2
rama export, 5.5.10
compound properties, 11.2
ramachandran plot, 5.5.9
prediction binding, 9.13
rmsd, 5.5.2
surface area, 5.5.5
preferred residues, 9.6
similarity, 5.7
tutorials, 21.3
presentations, 7
analysis, 21.3.4
preserve, 22.8.6
contact area, 21.3.5
press-and-hold to rotate, 10.4.8
convert, 21.3.2
pretty view, 16.3.6
hydrogen bond, 21.3.6
primary aliphatic amines, 10.15
icmpocketfinder, 21.3.7
principal component analysis, 17.5
search, 21.3.1
regression, 11
superimpose, 21.3.3
select, 5.4.1
display.distance, 6.9.1
sites by apf, 5.4.6
start color, 4.8
superimpose 3D, 5.4.3
quit, 3.6.1.19
grid, 5.4.5
multiple proteins, 5.4.4
table, 10.35.2
protein-protein, 5.6.6, 12.13, 12.13.1, 12.13.2, 12.13.3, 12.13.4, 12.13.5, 12.13.6, 12.13.8, 12.13.9, 12.13.10, 21.10
groups, 10.35.2
docking refinement, 12.13.11
protein-proteindocking, 12.13.7
decomposition, 10.28.7
convert, 9.21.1
enumeration, 10.28.7
protonated, 22.4.15
r-groups, 17.4.25
state, 12.1.4
radar, 17.4.6
states, 5.6.2
protonation_ph, 10.19
protonation_ph_charge, 10.19.2
protonation_ph_concentration, 10.19.1
range, 6.10.7.2
protprot, 12.13
rapid isostere replacement, 13.4
ratio.selection, 4.20.5
dock ligand, 16.9
pseudorotation P, 5.5.12
analysis, 5.5.12
reactive cysteine, 5.6.3
phase angle, 5.5.12
reactivity, 10.11.3
pubchem, 10.1
chemical, 10.1
publication quality images, 6.3.2
spreadsheet, 10.3.1
puckering amplitude, 5.5.12
split, 11.1.1
table, 17.1.2
pyramid, 12.1.6
pyramidal, 12.1.6
table, 17
qs hydrogen bond, 5.2.4
reagent, 10.35.5
pdb chem gl, 5.1.3.2
iw, 5.1.3.1
recent files, 3.6.1.17
pdb codes, 3.6.1.18
learn predict, 10.21
receptor, 5.2.2, 5.2.3, 10.6, 12.1, 12.6.2, 12.13.5, 12.13.7, 16.3.12, 21.12.1, 22.5.2, 22.5.14, 22.5.15
predict, 10.22
considerations, 12.1.1
quad buffer stereo, 22.1
flexibility, 16.15
buffer, 22.1.7
pocket, 16.3.1
flexibility, 21.12.2
molt, 18.4
recover, 3.6.2.11
processing, 10.5.3
setup, 10.5.1
quick, 4.15
image, 6.15.2
model multiple chain, 9.1.2.2
loops, 9.1.3
single chain, 9.1.2.1
side chain, 9.9
start move structure, 4.4
sidechains, 9.1.3
read pdb, 4.2
refinement, 12.6.4
representation, 4.7
region, 12.13.7
what is selected, 4.6.4
breaks, 6.1.3
cylinders, 6.1.3
covalent geometry, 12.2.1.3
smooth, 6.1.3
relaxed ligand, 16.3.9
worm, 6.1.3
ribbonColorStyle, 4.20.9
dock results, 12.4.5
ribose pseudorotation, 5.5.12
pucker, 5.5.12
salt, 22.8.14
ring, 5.5.12
explixit.hydrogens, 10.12
conformation, 5.5.12
salt, 10.12
torsion angles, 5.5.12
rename, 17.1.25
ride, 13.4
column, 17.1.25
gpu benchmark, 13.4.1.2
project, 3.6.1.9
server setup, 13.4.1.1
setup, 13.4.1
reorder column, 17.1.29
ridge, 13.5
replace chemical, 10.3.32
right, 4.13
replacement, 16.6
click, 4.13
group, 16.8
rigid, 10.37
report, 19.3
substructure superposition to template, 10.37.2
representation, 3.6.3.19
stacking, 5.2.5
alternative orientation, 21.3.11
content, 8.3.1
number selection, 22.2.36
pKa prediction, 5.6.2
speed, 6.10.7.2
pka, 5.6.2
root, 22.4.7
range, 4.6.18
mean square deviation, 5.5.2
chemical, 10.3.34
torsion, 6.12.6.1
when pasting, 10.4.8
mesh, 6.3.9.1
easy, 3.6.3.12
resolution, 4.2.4
speed, 6.10.7.2
rotating fragment in editor, 10.4.8
default, 22.1.9
rotation, 6.12.1
recent backup, 3.6.2.11
rotational symmetry axis, 5.5.11
restrained docking, 12.5
rough surface, 22.2.37
restraints, 14.2
flag, 17.1.13
results, 12.13.10
stack, 12.4.2
mark, 17.1.13
retrieve columns, 22.5.24
hide, 10.3.8
from original database, 22.5.24
show, 10.3.8
review and adjust binding site, 12.2.1.1
ruler, 6.8.16
rgroup, 10.35.4
molscreen, 15.1.2
rundock, 22.5.16
as a mesh object, 22.2.3
rxn, 10.4.13
faq, 22.2.23
safari, 22.3
preferences, 4.20.9
sali, 10.36.5
style, 4.20.9
bridge, 21.3.6
new project, 19.6
double bond cis trans, 12.2.1.3
pages, 19.7
query, 19.3
upload data, 19.2
racemic centers, 12.2.1.3
scare, 12.6.4
scatter, 13.1.9.2
analysis, 10.36
table, 10.36.3
threshold, 13.1.4
SMILES, 10.4.15
alignment, 8.7.3
PDB, 4.19
movie, 6.16.2
pdb, 4.19
chemical mol, 10.4.13
sculpting, 9.18
spreadsheet workspace, 10.2.1
sdf, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3.35, 10.10, 10.10.3, 10.20.1, 16.10, 18.1, 19.2, 21.11.2, 22.9.3, 22.9.4
to chemical spreadsheet, 10.4.14
docked ligand, 16.20
chembl, 4.16.2
file, 4.19
drugbank, 4.16.7
hits, 16.5.7
filter, 10.5.2
image plot, 17.4.21
in workspace, 3.6.2.4
ligand receptor complex, 16.20
pdb, 4.2.1
object, 4.10
ligand code, 4.16.6
pdb, 4.19
pocketome, 4.16.1
project icb, 4.11
pubchem, 4.16.8
sequence, 8.1.5
surechembl, 4.16.3
slide, 7.4
tab field, 4.2.4
smiles string, 10.4.15
pdb chemical, 4.2.2
table, 17.1.21
sequence, 4.2.3
spreadsheet, 16.5.7
tautomer, 10.5.3
tree, 17.7.3
uniprot, 4.16.5
sdf, 10.4.14
in.workspace, 3.6.2.4
secondary aliphatic amines, 10.15
object, 4.10
password, 3.6.1.11
picture, 3.6.1.15
a tree branch, 17.7.2
table.view, 17.1.8
all, 4.6.14
saving, 3.6.1.8
amino acid, 4.6.13
project, 3.6.1.8
duplicates, 10.33
scaffold, 10.14
molecule, 4.6.12
hopping, 16.8
neighbors, 4.6.15
graphic, 4.6.16
object, 4.6.11
hits, 12.4.1
group, 16.7
by number, 4.6.18
scan_pockets, 5.8
number, 4.6.18
scarab, 19
tree, 17.7.2
add user, 19.5
atom, 4.6.3
browse export data, 19.4
graphical, 4.6.3
installation, 19.1
object, 4.6.3
residue, 4.6.3
structure, 8.3.6
workspace, 4.6.3
type, 8.3.4
selectall, 3.6.2.3
DNA, 8.3.4
selecting.neighbors, 4.6.16
selection, 4.6.4, 4.6.5, 4.6.21, 6.3.4, 10.4.11, 17.4.18, 17.7.2, 17.7.4, 22.2.4, 22.2.6, 22.2.7, 22.2.8, 22.2.13, 22.2.32, 22.4.9, 22.4.10, 22.4.22, 22.5.14
amino acid, 8.3.4
clear, 3.6.2.7
nucleotide, 8.3.4
neighbors, 3.6.2.8
protein, 8.3.4
alignment, 4.6.19
search, 8.4
all, 3.6.2.3
alter, 4.6.7
atom, 3.6.2.5
unique, 8.3.13
basic, 4.6.2
extract, 8.3.13
change, 4.6.7
unique, 8.3.13
clear, 3.6.2.7
server, 13.1.7.2
column, 17.1.23
error, 22.1.17
graphical, 4.6.16
formal charges, 10.15
server, 22.1.17
level, 3.6.3.3
bond type, 9.21.5
mode, 3.6.3.4
charges, 9.21.6
near atoms, 3.6.2.8
chirality, 9.21.5
object, 4.6.11
bond, 9.21.5
other, 4.6.19
formal charge, 9.21.5
properties, 3.6.2.5
tether, 9.21.5
range, 17.1.23
types, 9.21.6
residue, 3.6.2.5
setAPFparams, 22.8.12
row, 17.1.23
setup, 12.13.6
sphere, 4.6.15
ligand receptor, 16.1
spherical, 3.6.2.8
superposition, 5.4.1
alignment, 21.4.4
shading, 6.3.12
elements, 17.1.23
shadow, 6.10.2
share model, 11.1.5
whole, 4.6.11
sheet, 22.2.20
shell preferences, 4.20.10
selectioninvert, 3.6.2.6
shift, 6.8.3
selections, 4.6
links, 8.3.9
shineStyle, 4.20.3
selectneighbors workspace, 4.6.17
organized network, 10.30
hide column, 17.1.39
sequence, 3.6.4, 4.2.3, 4.16, 4.16.4, 4.16.5, 4.17, 8, 8.1, 8.1.5, 8.2, 8.3, 8.3.7, 8.6.1, 8.6.5, 9.1.2, 10.4.17, 21.3, 21.4, 21.4.4, 22.4.12, 22.6, 22.6.1
side, 10.3.29
analysis, 8.3
by side, 10.3.29
editor, 8.5
error, 22.1.19
identity, 8.7.15
stereo, 3.6.3.6
pattern, 4.2.3
chain refinement, 16.14
reordering, 8.7.8
chains, 9.9
side-by-side, 22.1.19
similarity, 8.7.15
side-chain sampling, 12.13.11
sites, 8.5
side-chains, 12.6.1
similarity, 10.31
calculations, 9.21.18
length, 22.5.12
stacking, 5.2.5
simulations, 22.7
standalone hitlist, 12.4.4
single, 10.4.10
standard table, 17.1
chain, 9.1.2.1
standardize, 10.12
singlet, 10.4.7
table, 10.12
sites, 5.4.6
start, 10.10.2
size, 5.2.4.1
startup, 22.10.2
sketch accents, 6.10.3
static, 22.4.8
markush, 10.35.1
reaction, 12.8.1
bond, 10.4.2
smiles, 10.4.12
hardware, 3.6.3.7
side-by-side, 3.6.3.6
stereohard faq, 22.1.6
stereoisomer, 10.20.5
slice, 6.13
stereoisomers, 10.25
stick, 4.20.5
effects, 7.5
stl, 6.7
movie, 6.16.1
stop, 6.10.7.3
file, 7.2
navigation, 7.3.2
current view, 3.6.3.19
show, 7.3
faq, 22.2.22
blend, 7.5
edit, 7.4.1
strip, 22.4.9
effect, 7.5
smooth, 7.5
transition, 7.5
ensemble, 9.21.14
representation, 6.1
smiles, 10.20.4
smooth, 6.3.9.3
structure-based, 13
surface, 22.2.37
solid, 6.3.9.3
style, 4.20.5
solvent.accessible.area, 22.4.19
sort hitlist, 13.1.9.1
table, 3.6.10.4
template, 16.12.3
sorting, 13.1.9.1
alerts, 10.13
compounds, 17.7
sugar conformation, 5.5.12
sp3, 10.11.2
pucker analysis, 5.5.12
spec, 3.7.2
puckering, 5.5.12
specifications, 22.1.5
ring puckering, 5.5.12
specs, 1
sulfur, 9.10
faq, 22.1.5
speed, 6.10.7.2
3D, 5.4.3
sphere, 22.4.11
Calpha, 5.4.3
arrange.grid, 5.4.5
split, 10.36.1
backbone, 5.4.3
spreadsheet, 10.20.2
heavy atoms, 5.4.3
square, 22.4.7
multiple, 5.4.4
area, 5.5
zoom translate, 10.3.30
area, 5.5.5
action, 17.1.47
alignment, 17.1.12
surrounding, 22.4.11
append, 17.1.43
clone, 17.1.16
sxstrace, 22.1.19
color, 17.1.10
symmetric oligomer, 9.1.3
columns, 10.3.8
synthesize, 10.11.7
compare, 10.3.22
synthetic feasibility, 10.11.7
copy, 10.3.6
system preferences, 4.20.11
cursor, 17.1.47
pdb, 3.7.4
display, 22.10.4
table, 4.17, 10.1.3, 10.3.24, 10.3.25, 10.3.28, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.20.2, 10.23, 16.10, 17, 17.1.6, 17.1.35, 17.1.40, 17.1.45, 17.4, 17.4.1, 17.4.4, 17.4.9, 17.4.11, 17.4.13, 17.4.14, 17.4.15, 17.4.16, 17.4.17, 17.4.18, 17.4.20, 17.7.1, 22.4.19, 22.8.4, 22.8.5, 22.8.7, 22.8.8
double.click, 17.1.47
alignment, 17.1.12
edit, 10.3.17
clone, 17.1.16
color, 17.1.10
column format, 17.1.40
find-replace, 10.3.13
to screen, 17.1.4
delete, 17.1.17
font, 17.1.11
edit, 17.1.24
foreground, 22.10.4
filter, 17.1.43
grid lines, 17.1.4
find, 17.1.9
hide, 17.1.39
replace, 10.3.32
hyperlink, 10.3.15
font, 17.1.11
insert, 17.1.33
size, 22.2.1
join, 3.6.10.5
grid, 17.1.5
label, 10.3.14
histogram, 17.4.1
landscape, 17.1.18
insert, 17.1.26
mark, 10.3.14
layout, 17.1.5
learning, 17.6
mouse, 17.1.47
mark, 17.1.13
name, 17.1.15
row, 17.1.13
new, 17.1.1
mouse, 17.1.47
options, 17.1.14
navigation, 17.1.4
orientation, 17.1.18
new column, 17.1.26
portrait, 17.1.18
plot, 17.4
print, 17.1.19
read, 17.1.2
rename, 17.1.15
rename, 17.1.15
rightclick, 17.1.14
right click, 17.1.14
row height, 22.2.39
row, 17.1.33
save, 17.1.3
rows, 3.6.10.7
selection, 17.1.3
search, 17.1.9
scale, 17.1.18
select, 17.1.23
scroll, 17.1.4
setup, 17.1.18
sdf, 10.3.9
sort, 17.1.42
select, 17.1.23
split fragments, 10.3.33
setup, 17.1.18
view, 17.1.5
save, 17.1.8
standard, 17.1
width, 17.1.4
background, 6.15.3
ribbon, 22.2.3
surface, 22.2.37
tags, 4.6.21
m, 5.5.12
branch swapping, 8.7.8
distance, 10.28.3
tautomers, 10.24
edit, 10.28.4
temperature, 5.6.5
reorder, 10.28.3
triplet, 10.4.7
docking, 22.5.3
trouble shooting, 22.1.11
templates, 10.4.6
trouble-shooting, 22.1.12
terminal, 10.3.28
truncating a mesh object, 22.2.15
font size, 22.2.1
crash qlock, 22.1.13
tsv, 17.1.21
tut analyze alternative orientations, 21.3.11
search, 10.5.4
occupancy, 21.3.10
texture, 3.7.6
symmetry, 21.3.9
multiple receptor, 21.12.1
tut3, 21.5
threshold, 4.20.5
tut3e, 21.3.12
tier, 4.14
tut5a, 21.9.1
time, 22.5.11
tut5b, 21.9.2
machine, 22.1.15
tut5c, 21.11.1
tissue, 4.16.9
tut5e, 21.11.2
racemic, 10.20
tutorial 2D pharmacophore, 21.6.6
tools 3D, 3.6.6
3D pharmacophore, 21.6.5
analysis, 3.6.7
chemical clustering, 21.6.3
append rows, 3.6.10.7
search, 21.6.2
extras, 3.6.9
molecular documents, 21.2
plot function, 3.6.9.1
sequence alignment, 21.4
superimpose, 3.6.8
link, 21.4.2
table, 3.6.10
load sequence, 21.4.1
Learn, 3.6.10.1
sequence conservation, 21.4.3
clustering, 3.6.10.3
tutorials, 21
merge, 3.6.10.5
predict, 3.6.10.2
ubuntu, 22.1.18
tooltip, 17.4.26
ultra large library, 13.5
balloons, 17.4.26
analysis, 10.16
box shade font, 8.7.7.1
undisplay-all, 3.6.3.1
free strain, 10.17
origin, 6.8.12
scan, 9.21.7
toxscore, 10.11.3
redo, 16.5.5
trace, 6.1.10
transition.blend, 22.2.31
unit, 5.3.3
units, 22.5.1
unix, 22.10.2
transparent, 6.3.9.3
unsatisfied hydrogen bonds, 16.3.8
upload, 19.2
run, 13.1.6
use activeicm, 7.12
score, 12.1.9
visualization, 13.1.11
defined groups, 16.5.3
results, 13.1.8
modifiers, 16.5.3
volume, 10.4.9
user-defined groups, 10.4.5
van der waal, 6.8.15
waters, 9.21.17
verbose, 10.23
weak, 22.4.20
large sdf files, 10.1.2
web, 21.2
vicinity, 10.23
browser, 3.6.1.12
weighted, 17.7.1
animate view, 3.6.3.15
width, 17.1.22
center, 3.6.3.20
window, 4.14
color background, 3.6.3.18
dock results, 12.4
fog, 3.6.3.5
wireBondSeparation, 4.20.1
macroshape, 3.6.3.22
working directory, 22.5.23
menu, 3.6.3
mesh clip, 6.13.1
panel, 4.5
perspective, 3.6.3.9
selection, 4.6.9
selection level, 3.6.3.3
navigation, 4.6.10
mode, 3.6.3.4
shadow, 3.6.3.13
alignment, 8.7.3
sketch accents, 3.6.3.14
excel, 10.2.3
slide show, 7.3.1
tools, 3.6.3
images, 6.15
tree, 17.7.4
pdb, 4.19
undisplay all, 3.6.3.1
image, 3.6.1.15
stach, 9.21.15
object, 4.10
picture, 3.6.1.15
ligand screening, 15
table, 17.1.3
writing a pdb file, 22.4.3
examples, 21.11
ray, 3.6.5
virus, 5.3.3
visualize, 10.30
xls, 10.2.3
apf fields, 16.3.11
xlsx, 10.2.3
chemical space, 10.30
xml, 19.2
ligand strain, 16.3.10
vls, 12.6, 12.6.3, 13, 13.1, 13.1.6, 13.1.7.2, 13.1.9.4, 13.3, 14.4, 21.11.2, 22.5.7, 22.5.8, 22.5.24
xyz, 22.2.10
analysis, 13.1.9.4
youtube, 2
display, 13.1.9.3
command line, 13.1.7.2
τm, 5.5.12
getting started, 13.1.2
histogram scatter plot, 13.1.9.2
introduction, 13.1.1
preferences, 13.1.4
results, 13.1.8