Index
Blast, 22.2.25
Chemical Label, 6.8.11
BlastDB Directory, 4.7.2
Interaction Diagram, 16.3.7
alphas, 6.8.3
bioisostere, 10.9.1
CHEMRIYA, 13.5
chemical label, 6.8.11
COLLADA, 3.6.1.7
from PDB, 10.1.1
CPK, 3.7.1
interaction diagram, 10.6
screening, 15
Chemical Cluster, 21.6.3
Search, 21.6.2
depiction, 10.20.2
CisTransAmide Angle, 13.1.9.4
Clash Threshold, 4.7.10
Computational Chemistry, 16.20
Computer-Aided Drug Discovery (CADD), 16.20
interactive ligand editor, 3.7.5
Covalent Geometry., 16.20
ligand editor, 16.3.4
object, 6.3.9
Decomposition, 10.36.3
Design Evolution, 12.10
print, 6.7
Display, 22.2.26
printing, 6.7
Distance, 13.1.9.4
screening, 15
Dock Directory, 4.7.2
stereo, 6.6
Docking, 22.2.26
3DMOLT, 18.5
Drug Bank, 4.2.8
3DQsar, 11.4
Design, 16.20
3D_Similarity_PDB_Search, 5.7
Editor, 4.7.2
3Dqsar tutorial, 21.14
Eintl, 12.1.10
bioisostere, 10.9.2
Error in saving configuration settings: You are not a license administrator, 22.1.10
predict, 5.6
Extended Amino Acids, 16.20
helices strands, 5.6.1
FILTER.Z, 4.7.2
local flexibility, 5.6.4
gz, 4.7.2
protein health, 5.6.3
uue, 4.7.2
tools identify ligand binding pocket, 5.6.6
FTP.createFile, 4.7.11
oda, 5.6.5
keep File, 4.7.11
proxy, 4.7.11
dock, 16.15
Filter.zip, 4.7.2
docking, 4.2.2
Flexible Minimization, 16.20
64, 22.1.3
Force Auto Bond Typing, 4.7.11
AI, 12.10
Free Wilson, 10.36.2
template, 10.37.3
Frequently Asked Questions, 22
Acetyl Cap, 16.20
GAMESS, 9.21.16
ActiveICM, 3.6.1.12
Alpha-Helix Stabilization, 16.20
GINGER, 10.23
GPCR Modeling Example, 21.5.1
Atom Single Style, 4.7.3
GRAPHIC.store Display, 4.7.3
NtoC Rainbow, 4.7.4
alignment Rainbow, 4.7.4
Baell, 10.4.9
atomLabelShift, 4.7.7
Beep, 4.7.11
ballStickRatio, 4.7.1
Beta-Catenin, 16.20
center Follows Clipping, 4.7.3
Bioactive Conformation, 16.20
clash Style, 4.7.3
clip Grobs, 4.7.3
wire Width, 4.7.1
Skin, 4.7.3
wormRadius, 4.7.9
Static, 4.7.3
xstick Backbone Ratio, 4.7.1
discrete Rainbow, 4.7.4
Hydrogen Ratio, 4.7.1
displayLineLabels, 4.7.7
Style, 4.7.1
displayMapBox, 4.7.3
Vw Ratio, 4.7.1
distance Label Drag, 4.7.1
GROB.arrowRadius, 4.7.3
dnaBallRadius, 4.7.9
atomSphereRadius, 4.7.3
dnaRibbonRatio, 4.7.9
contourSigmaIncrement, 4.7.3
dnaRibbonWidth, 4.7.9
relArrow Size, 4.7.3
dnaRibbonWorm, 4.7.9
relArrowHead, 4.7.3
dnaStickRadius, 4.7.9
GUI.auto Save, 4.7.4
dnaWormRadius, 4.7.9
Interval, 4.7.4
font Scale, 4.7.7
autoSave, 22.2.33
fontColor, 4.7.7
autoSaveInterval, 22.2.33
fontLineSpacing, 4.7.7
enumeration Memory Limit, 4.7.11
grobLineWidth, 4.7.3
max Nof Recent Files, 4.7.11
hbond Ball Period, 4.7.1
Sequence Length, 4.7.4
Style, 4.7.1
splash Screen Delay, 4.7.11
hbondAngleSharpness, 4.7.1
Image, 4.7.11
hbondMinStrength, 4.7.1
table Row Mark Colors, 4.7.4
hbondStyle, 4.7.1
workspace Folder Style, 4.7.4
hbondWidth, 4.7.1
workspaceTabStyle, 4.7.4
hetatmZoom, 4.7.1
GigaScreen, 18.5
hydrogenDisplay, 4.7.1
light, 4.7.3
lightPosition, 4.7.3
HTTP.proxy, 4.7.11
mapLineWidth, 4.7.3
support Cookies, 4.7.11
occupancy Radius Ratio, 4.7.3
user Agent, 4.7.11
occupancyDisplay, 4.7.3
Hbond to selection, 13.1.9.4
quality, 4.7.3
Hbonds, 16.3.4
rainbow Bar Style, 4.7.4
Helicon Peptide, 16.20
resLabelDrag, 4.7.7
How To Guide, 3
resize Keep Scale, 4.7.3
Html, 4.2.1.6
ribbonRatio, 4.7.9
Http Read Style, 4.7.11
ribbonWidth, 4.7.9
Hydrocarbon Staples, 16.20
ribbonWorm, 4.7.9
Hydrogen.bond, 4.7.5
rocking, 4.7.4
I+4 Staple Position, 16.20
Range, 4.7.4
Staple Position, 16.20
Speed, 4.7.4
ICM Browser How To, 3.1
selectionStyle, 4.7.3
Pro How To, 3.2
site Label Drag, 4.7.7
graphics crash, 22.1.11
Shift, 4.7.7
start, 1
siteArrow, 4.7.7
ICM-Pro Tutorial, 16.20
stereoMode, 4.7.3
IMAGE.bondLength2D, 4.7.6
stickRadius, 4.7.1
color, 4.7.6
surfaceDotDensity, 4.7.3
compress, 4.7.6
surfaceDotSize, 4.7.3
gammaCorrection, 4.7.6
surfaceProbeRadius, 4.7.3
generateAlpha, 4.7.6
transparency, 4.7.3
lineWidth, 4.7.6
orientation, 4.7.6
MolVol, 10.11
paper Size, 4.7.6
Molcart, 10.5.3
previewResolution, 4.7.6
previewer, 4.7.6
Molecular Docking, 16.20
print, 4.7.6
Preparation, 16.20
printerDPI, 4.7.6
Movie.fade Nof Frames, 4.7.4
scale, 4.7.6
quality, 4.7.4
stereoAngle, 4.7.6
Auto, 4.7.4
stereoBase, 4.7.6
NCBI, 22.2.25
stereoText, 4.7.6
NH2 Cap, 16.20
INCHI, 10.20.3
NVIDIA, 22.1
IQR, 17.4.6
Natural Amino Acids, 16.20
ISIS, 22.8.3
Nof_Atoms, 10.11
Icm Prompt, 4.7.10
Nof_Chirals, 10.11
Nof_HBA, 10.11
key, 10.3.20
Nof_HBD, 10.11
Interaction Diagram 2D, 16.3.7
Nof_Rings, 10.11
Interactive Ligand Editor, 16.20
Nof_RotBonds, 10.11
Internal Coordinates Table, 9.21.13
Non-overlap, 13.1.9.4
Directory, 4.7.2
Nvidia GL failutre, 22.1.11
JPEG, 3.6.1.15
ODA, 22.2.26
KMZ, 3.6.1.7
Optimal, 22.2.26
LCC, 13.5
Output Directory, 4.7.2
LigStrain, 16.20
Ligand Strain, 16.20
chemicals, 10.4.9
Log Directory, 4.7.2
analysis, 10.29
7UWI, 16.20
Directory, 4.7.2
MOL2, 13.1.3
Style, 4.7.2
MOLT, 18.1
link, 17.1.40
MOVIE.frame Grab Mode, 4.7.4
MPO, 10.34
Field, 3.6.2.13
Mac, 22.1.15
Homology, 3.6.2.15
Atom Margin, 4.7.10
Identity, 3.6.2.14
Sigma Level, 4.7.10
Sequence, 3.6.2.16
Markush, 21.6.9
convert, 5.1.2
create, 21.6.7
PFAM, 3.6.1.7
File Size Mb, 4.7.11
PLOT.Yratio, 4.7.8
Max_Fused_Rings, 10.11
color, 4.7.8
Mnconf, 4.7.10
date, 4.7.8
Model, 11.4
draw Tics, 4.7.8
MolCart, 22.9
font, 4.7.8
fontSize, 4.7.8
labelFont, 4.7.8
lineWidth, 4.7.8
MolPSA, 10.11
logo, 4.7.8
MolScreen, 15
markSize, 4.7.8
MolSoft ICM-Pro, 16.20
orientation, 4.7.8
previewer, 4.7.8
SEQUENCE.site Colors, 4.7.4
rainbowStyle, 4.7.8
SITE.label Style, 4.7.7
seriesLabels, 4.7.8
labelOffset, 4.7.7
PLS, 11.1
wrap Comment, 4.7.7
SLIDE.ignore Background Color, 4.7.4
PROTAC, 12.14
Fog, 4.7.4
PSA, 10.11.7
Peptide Engineering, 16.20
Mode, 16.20
Select Min Grad, 4.7.10
Modeling, 16.20
Sequence Editing, 16.20
Stapling, 16.20
Show Res Code In Selection, 4.7.7
Pharmacophore RMSD, 13.1.9.4
Sidechain Optimization, 16.20
Projects Directory, 4.7.2
Special Cases, 10.34.1.1
Prosite Dat, 4.7.2
Strain, 12.4.3.1
Protein, 22.2.26
SureChEMBL, 4.2.4
Protein-Peptide Interactions, 16.20
Swissprot, 3.6.1.7
Viewer, 4.7.2
Dat, 4.7.2
Pub Chem, 4.2.9
link, 17.1.40
PubMed, 4.2.1.7
Temp Directory, 4.7.2
Reference, 17.1.40
Terminal Capping, 16.20
Pubchem, 4.2.9
Torsion Minimization, 16.20
USER.email, 4.7.11
friends, 4.7.11
and S, 22.5.21
full Name, 4.7.11
R-Group, 10.36.3
organization, 4.7.11
R-groups, 16.5.3
phone, 4.7.11
Ultra Large Libraries, 18.5
RIDE, 18.5
Uniprot, 17.1.40
RIDGE, 18.5
VHL, 12.14
- Rapid Docking GPU Engine, 13.5
preferences, 13.1.4
RMSF, 9.21.18
Van Drie, 10.36.5
RNA, 4.3
Label Style, 4.7.7
Score, 16.20
Change, 13.1.9.4
Ramachandran Plot, 5.5.9
Water Radius, 4.7.10
Real Format, 4.7.10
Wilson, 10.36.2
Reinforce Helix Tool, 16.20
Wire Style, 4.7.1
Relax Geometry Command, 16.20
XPDB Directory, 4.7.2
Label Shift, 4.7.7
Xstick, 3.7.1
Style, 4.7.7
a-bright, 3.7.2
Residue Replacement, 16.20
about model, 11.1.3
activeICM, 7.8
SCARE, 12.6.4
advanced, 7.14
background images, 7.15
control, 7.13
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
album, 6.15.3
view, 8.7.10
alias, 10.4.5
allosteric, 5.6.6
color 2D scaffold, 10.14
alpha, 3.7.2
dna protein, 8.6.4
channel, 4.7.6
multiple, 8.6.5
ambient, 3.7.2
sequence structure, 8.6.3
amidinium, 10.15
two sequences, 8.6.2
amino acid, 4.3
DNA to protein, 8.6.4
acids, 10.4.6
stereo faq, 22.1.8
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
annotation tutorial, 21.4.4
box shade font, 8.7.7
angstrom, 22.4.7
editing, 8.7.1
editor, 8.7
view, 6.10.7
example, 8.3.14
font size, 22.2.1
store, 6.10.7.4
format, 8.7.11
animations, 7
gaps, 8.7.11
image, 8.7.2
alignment, 8.7.6
profile, 21.4.4
by substructure, 10.13
reorder, 8.3.12
plot, 17.4.24
search, 8.7.12
annotation, 8.7.6
secondary, 21.4.4
lines, 3.6.3.17
selection, 8.7.13
lines, 3.6.3.17
strength, 8.3.8
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
profile, 8.3.8
flexible template, 10.37.6
view options, 8.7.10
pairwise, 10.37.5
color, 8.7.9
super, 10.37.3
comment, 8.7.6
template, 16.12.3
tools, 10.38
cut, 8.3.11
3DQSAR, 10.38.4
display title, 8.7.10
consensus ph4, 10.38.1
editor, 8.7
pairwise score, 10.38.2
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, 4.7.5
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
applying prediction models, 11.2
basicsel, 4.6.2
file, 12.3.2.2
arrange, 4.1.13.1
index, 12.3.2.4
window, 4.1.13.1
loaded icm object, 12.3.2.1
graph, 22.2.8
mol mol2, 12.3.2.3
as2_graph, 4.6.5
molcart, 12.3.2.5
as_graph, 22.2.8
run, 12.3.3
asparagine, 9.21.2
bayesian classifier, 11
assign, 6.1.3
bbb, 10.11.4
2D coordinates, 10.20.2
beep, 22.2.35
helices, 5.6.1
begin docking simulation, 12.3
strands, 5.6.1
best, 10.3.34
bicyclics, 10.4.6
charge, 22.4.21
atomLabelStyle, 4.7.7
properties, 6.3.1
atomic energy circles, 16.3.5
bioinfo align multiple, 8.3.7
two sequences, 8.3.5
score, 10.38.2
links, 8.3.9
menu, 3.6.4
secondary structure, 8.3.2
point, 10.35.4
translation, 8.3.3
author, 4.2.1.3
bioisoester, 10.9
close tree, 10.28.5
play slide, 7.13
biological, 5.3.3
autofit, 12.11
autosave, 22.2.33
bit, 22.1.3
available properties, 10.11.1
ave, 17.7.1
search, 4.2.5
blood brain barrier, 10.11.4
axes, 17.4.15
blue lines, 8.2
axis, 17.4.11
boat, 22.5.20
options, 17.4.10
grid, 17.4.10
covalent, 22.4.2
range, 17.4.10
title, 17.4.10
bonding, 6.1.8
preferences, 4.7.1
coloring scale, 22.2.38
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
bye, 3.6.1.19
edit buttons, 10.4.11
alpha, 6.1.10
trace, 6.1.10
not starting, 22.1.13
ca-trace, 6.1.10
fingerprint, 15
cache, 7.14.1
fingerprints, 22.8.15
fragments, 10.3.33
properties, 10.11
group, 10.4.5
sequence similarity, 8.7.15
startup, 22.10.2
modifiers, 10.35.2
properties, 21.6.4
carboxylic acid, 10.15
right click, 10.4.3
cartesian, 10.23
cation, 5.2.5
filter, 10.5.2
cavities, 5.5
text, 10.5.4
closed, 5.5.4
sketch, 21.6.1
space, 10.30
cell, 5.3.2
compare, 10.3.22
on ligand, 16.3.13
template, 10.3.2
and representative members, 17.7.2
spreadsheets, 10.3
cereblon, 12.14
substituent, 10.9
chain.breaks, 22.2.34
substructure, 4.2.1.1
chair, 22.5.20
change box size, 16.9.1
display, 10.3.3
height of all rows, 17.1.7
tables, 17.2
ligand, 16.5.1
toxicity, 10.11.3
residue number, 9.2
2D, 10.7
row height, 17.1.7
3D, 10.7
selection, 4.6.7
append, 10.4.13
speed range, 6.10.7.2
changing font in alignment editor, 8.7
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
display.fit, 22.8.13
draw, 10.4.1
check box, 7.6.6
duplicates, 10.3.21
convert, 22.8.5
export excel, 10.2.3
load, 10.1
save, 10.2
merge, 10.32
3D, 10.2.5
new, 10.4.1
editor, 10.2.4
properties, 10.3.19
read, 10.1
downstream cluster, 10.28.5
project, 16.22
cavities, 5.6.6
structure, 10.4.13
stack, 9.21.18
representative.center, 10.28.2
cns, 10.34
tutorials, 21.6
color, 5.6.3, 6.3.2, 6.3.3, 6.3.4, 6.3.9.4, 6.4, 6.4.1, 6.8.2, 6.8.3, 8.8, 10.3.35, 10.14, 17.1.45, 17.7.4, 22.2.4, 22.2.5, 22.2.16, 22.2.20
convert, 10.20
alignment, 8.7.9
2dto3d, 10.20.1
background, 6.4.2
pca, 10.29
by, 6.4
smiles, 10.20.3
alignment, 8.8
duplicates, 10.33
chemical, 10.3.35
remove.redundant, 10.33
faq, 22.2.20
chemlib.so, 22.1.3
key, 22.2.38
chemspace, 10.5.5
scale, 22.2.38
append, 21.6.4.4
surface by proximity, 6.3.3
build visualize, 21.6.4.1
selection, 6.3.4
compare, 21.6.4.8
table, 10.3.27
delete row, 21.6.4.3
2D sketch, 10.5.6.5
distinguish, 21.6.4.7
export, 21.6.4.5
distance, 6.8.10
project, 21.6.4.6
mesh, 6.3.9.3
select, 21.6.4.2
table, 10.3.27
coloring, 6.4.1
chimeric ligands, 12.9
annotation, 17.1.41
order, 17.1.29
considerations, 12.1.3
plot, 17.4.6
chrome, 22.3
row width, 17.1.22
cis trans proline, 21.5.2
statistics, 17.1.32
visibility order, 17.1.28
volumes, 13.1.11
color, 17.1.10
classes, 10.3.28
hide, 10.3.8
classification model, 15.5
show, 10.3.8
clear display and planes, 3.6.3.2
combinatorial chemistry, 10.35
selection, 4.6.6
library, 21.6.8
planes, 3.6.3.2
combine, 3.6.10.5
display style, 4.7.9
command, 22.5.16
line, 22.2.32
clipping, 22.2.19
commands, 22.10.1
planes, 6
common substructure, 10.37.1
tool, 6.13
compact tree, 10.28.5
tools, 6.13
clone, 3.6.1.2
table, 10.3.22
tables, 10.31
tutorial, 21.9.3
compounds, 22.9.3
crash, 3.6.2.11
compress, 4.7.6
creat, 7.6.1
compressed, 17.1.6
create, 17.1.1
table view, 17.1.6
markush, 10.35.3
conditions, 10.5.2
new objects, 4.3
gen, 10.23
cross, 22.2.10
configuration error, 22.1.19
section, 6.13
cryptic, 5.6.6
conformational entropy, 10.27
crystal, 5.3.2
conformations, 22.9.8
crystallographic analysis, 5.3
conformers, 10.23
biomolecule, 5.3.3
contour map, 5.3.6
object, 6.12.7
convert2grid, 5.3.7
crystallographic cell, 5.3.2
load eds, 5.3.4
pharmacophore, 10.38.1
maps cell, 5.3.5
symmetry packing, 5.3.1
molecule, 3.6.1.1
tools, 21.3.8
object, 3.6.1.1
cell, 3.6.5
neigbor, 5.3.1
surface, 6.3.2
neighbors, 3.6.5
current, 22.2.22
chemical, 10.3.24
slide, 7.13
2D 3D, 10.7
curves, 17.4.5
3D molecular editor, 10.4.16
from pdb, 5.1.3
actions, 17.1.40
local database, 3.6.1.6
fragments, 10.13
pdb, 21.3.2
label, 6.8.8
chem, 10.7.1
rotation, 6.12.2
smiles to 2D, 22.8.11
customized MPO score, 10.34.1
local.database, 3.6.1.6
cut, 17.1.35
vertical alignment block, 8.3.11
converting pdb, 5.1.2
cyclic peptide, 9.20
coordinates, 10.1.3
cys, 5.6.2
cysteine reactivity, 5.6.2
cell, 17.1.36
damaged skin, 22.1.12
chemical, 10.3.25
dash, 22.2.12
loop, 9.5
paste row, 17.1.35
file format, 13.1.3
row, 17.1.36
search and alignment, 8.4
rows, 17.1.44
databases, 22.9.3
selection to table, 17.1.37
novo, 12.10
chemical, 10.3.16
design, 12.9
covalent, 16.10.1
decompose.library, 21.6.9
decoration, 16.18
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
selection, 3.6.2.1
meshes, 6.3.5
tether, 9.21.5
and display.macroshape, 3.7.6
dendrogram, 10.30.1
molecule, 10.3.24
denovo, 12.9
origin, 6.8.12
potential, 3.6.3.21
representations, 3.7.1
deselect, 22.2.7
restraints, 6.8.14
ribbon, 6.1.3
deviation, 22.4.7
skin, 6.1.4
dfa, 15.3.3
status, 22.2.32
dfz, 15.3.2
dialog, 7.6.5
surfaces, 3.7.6
diffuse, 3.7.2
table, 10.3.3
tethers, 6.8.13
angle, 5.5
wire, 6.1.1
dimensional, 22.8.6
xstick, 6.1.2
directories preferences, 4.7.2
directory, 4.7
faq, 22.4.10
disappearing labels, 22.1.12
restraint, 12.5
dislay ligand receptor interaction, 10.6
label, 4.7.7
display, 4.1.4, 4.1.13.1, 4.7, 5.2.3, 5.2.3.1, 5.2.3.2, 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
distances, 3.7.3
chemical, 6.8.11
delete distances, 6.9.4
bonds, 9.17
dihedral, 6.9.3
diverse set, 17.7
distance restraints, 6.8.14
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
distance2, 6.9.1
apf, 16.17
angles, 6.9
chemical table, 12.3.4
formal charge, 6.1.9
command, 22.5.16
gradient, 6.8.17
macrocylce, 22.5.20
hbond, 13.1.9.3
start, 12.1
table, 16.10
hydrogen, 6.1.7
covalent, 16.10.1
atoms ligand editor, 16.3.3
docked ligand strain, 12.1.10
mesh, 6.3.5
docking, 5.6.5, 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
meshes, 6.3.8
batch index, 12.3.2.4
options, 16.3
covalent, 12.8
planar angle, 6.9.2
display, 12.4.6
explicit group, 21.12.2
macrocycles, 12.2.1.3
preferences, 12.2.1.3
like, 10.11.4
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, 4.1.8
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
template, 12.7
alignment, 8.7.1
templates, 16.12.3
chemical moledit, 10.3.26
tutorials, 21.9
waters, 12.1.8
2D, 16.5.1
background, 22.5.19
editor preferences, 16.2
batch, 12.3.2
multiple substituents, 16.5.2
conformations, 22.5.20
tools, 3.6.2.17
flexible.rings, 22.5.20
menu, 3.6.2
hitlist, 12.4.3
molecular document, 7.6.1
interactive, 12.3.1
molecule, 10.4
preparation, 12.2.1
molt, 18.3
procedure, 12.3
selection, 3.6.2.5
rank, 12.4.3
slide, 7.4.1
table row, 17.1.24
sampling, 22.5.20
molecule, 10.3.26
score, 12.4.3
structure, 10.3.26
stack, 12.4.2
editor, 22.4.12
template, 12.7
editpdbsearch, 3.6.2.12
navigation, 7.6.7
documents, 6.15.3
on binding tutorial, 21.5.3
dollar, 22.10.3
example2, 21.5.3.1
donator, 10.4.9
stability tutorial, 21.5.4
envelope, 3.7.1
surface, 4.7.5
dotted line, 6.1.3
denisty map, 5.3.5
lines, 22.2.34
double, 10.4.10
contour, 3.6.5
doublet, 10.4.7
electrostatic coloring scale, 22.2.38
potential, 3.6.3.21
dpc, 15.3.4
surface, 6.3
and drop sequences, 8.6.6
elegant sketch, 6.10.4
residue label, 3.6.3.16
element, 10.4.10
draganddrop, 4.1.11
eln, 19.7
embed browser, 7.11
chemical, 10.4.1
powerpoint03, 7.8
powerpoint07, 7.9
activeicm, 7.13
script, 7.13
ISISdraw, 22.8.3
MolCart, 22.9
activeicm, 22.3
path, 22.3.3
microsoft, 7.7
alignment secondary structure, 22.6.2
apf model, 22.8.12
empty hostid, 22.1.18
atom charge, 22.4.21
enamine, 10.5.5
display, 22.2.17
real, 13.5
autosave, 22.2.33
enantiomer, 22.5.21
backbone, 22.2.13
enantiomers, 12.1.3
background color, 22.2.2
job, 22.5.19
circles, 13.1.11
beep, 22.2.35
binding energy, 22.5.2
terms, 9.21.19
blend transition, 22.2.31
ensemble, 12.6.2
breaks, 22.2.34
calculations, 9.21.18
change torsion, 22.4.16
chem table display, 22.8.4
enumerate formal charge states, 10.18
chemical monitor, 22.8.10
reaction, 21.6.10
query2, 22.8.1
enumeration, 10.35.4
cheminformatics, 22.8
eps, 10.2.6
clipping plane, 22.2.11
epsilon, 22.4.15
closest, 22.4.22
eraser, 10.4.11
color carbon, 22.2.4
errno, 22.1.3
skin, 22.2.16
command line display, 22.2.32
evaluate score strain, 16.4
convert chemical from pdb, 22.4.1
exact, 10.31
covalent bond, 22.4.2
excel, 10.2.3
delete, 22.4.9
exclude fragment, 10.5.2
descriptors, 22.8.15
volume, 16.3.11
deselect, 22.2.7
exit, 3.6.1.19
dihedral, 22.2.18
dock charge groups, 22.5.22
flex, 12.6.1
probe, 22.5.13
group, 12.6.3
racemic, 22.5.21
docking, 12.6.3
repeat, 22.5.5
groups, 21.12.2
working directory, 22.5.23
docking, 22.5
dock project, 16.21
docktime, 22.5.11
pdb, 4.5
dollar, 22.10.3
extra windows, 6.2
download install, 22.1.1
druglikeness, 22.8.9
2D, 10.1.1
energy, 22.5.1
3d coordinates to spreadsheet, 10.1.3
error admin, 22.1.10
icb, 3.6.1.5
extract ligand, 22.8.8
object icb, 4.4.2
flexible dock, 22.5.15
sub alignment, 8.3.10
ring docking, 22.5.20
icb, 3.6.1.5
font size, 22.2.1
pharmacophore, 10.5.6.4
foreground table, 22.10.4
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
measure distance ring, 22.8.16
faqhbondstrength, 22.2.29
merge, 22.4.5
faqmaps, 22.2.27
modeling, 22.7
faqoda, 22.2.26
molcart 64bit, 22.1.3
faqstereo, 22.1.14
query, 22.9.5
fasta, 8.1.5
sdf, 22.9.4
fbdd, 13.2
text search, 22.9.6
fft, 12.13.1
molecule c, 22.2.5
protein protein docking, 12.13.1
moledit, 22.8.2
file, 3.6.1.3
movie planes, 22.2.19
close, 3.6.1.13
newscript, 22.10.1
compatible, 3.6.1.10
nmr, 22.4.18
export, 3.6.1.12
nvidia error, 22.1.2
high quality image, 6.15.1
origin, 22.2.10
load, 3.6.1.7
plist, 22.1.9
menu, 3.6.1
pmf score, 22.5.6
password, 3.6.1.11
pockets, 22.2.14
preferences, 3.6.1.16
preserve coordinates, 22.8.6
quick image, 3.6.1.14
quad buffer, 22.1.7
icb, 4.1.10
receptor selection, 22.5.14
recent, 3.6.1.17
reload dock, 22.5.4
bak, 3.6.2.11
remove salt, 22.8.14
select, 22.2.6
selection, 4.6.8
renumber, 22.4.4
filters, 13.1.5
residue number selection, 22.2.36
find chemical, 10.3.32
rmsd, 22.4.7
rmsdtips, 22.4.8
method, 11.3
rocking active ppt, 22.3.1
fingerprints, 22.8.15
speed, 22.3.2
firefox, 22.3
rotate chemical, 22.8.13
scale display, 22.2.38
scanScoreExternal, 22.5.17
scanScoreExternal2, 22.5.18
score, 22.5.8
APF superposition to template, 10.37.4
script, 22.10
docking, 16.13
sequence secondary structure, 22.6.1
receptor groups, 16.13
alignments, 22.6
ring sampling level, 12.2.1.3
smiles, 22.8.11
flood, 9.21.17
solvent accessible surface table, 22.4.19
ss, 22.4.17
labels, 21.1.3
form view, 17.1.5
user interface, 22.2
graphics, 4.1
card, 22.1.2
controls, 6
defects, 22.1.12
effects, 6.10
linking, 16.11
panel, 6.2
screening, 13.2
preferences, 4.7.3
fragments, 10.8
frame, 8.3.3
radical, 10.4.7
wilson regression analysis, 10.36.2
freedomspace, 10.5.5
freeze column, 17.1.30
column, 17.1.46
row, 17.1.31
groupGen, 16.18
frequency, 10.3.35
guanidinium, 10.15
full model, 9.1.3
builder, 9.1.3
menus, 3.6
multiple chain, 9.1.3.1
preferences, 4.7.4
refinement, 9.1.3
tabs, 3.7
scene antialias, 3.6.3.10
screen, 3.6.3.8
halogen, 10.11.2
functional.groups, 10.13
fuzzy, 12.7
hba, 13.1.10
gap, 9.4
hbd, 13.1.10
general preferences, 4.7.5
generalselecttools, 4.6.1
strength, 22.2.29
getting started, 4
health, 5.6.3
giga search, 10.5.5
heatmap, 17.4.7
sized library, 13.5
example, 17.4.7.1
gigasearch, 10.5.5
helix, 22.2.20
ginger, 10.23
help, 2
videos, 2
glutamine proline, 9.21.2
hetero, 10.3.28
google, 3.6.1.7
scan, 16.7
objects, 6.3.7
hidden block format, 8.7.11
width, 8.7.11
gpcr_model, 21.5.1
hide, 17.1.39
graft loop, 9.5
column, 17.1.28
graphical, 22.2.4
high, 3.6.1.15
quality, 3.6.3.11
tutorial, 21.1
highlight new data, 10.3.7.1
2D3D labels, 21.1.4
his, 22.4.15
annotation, 21.1.2
color representation, 21.1.1
tautomer, 22.4.15
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, 4.2.10
labels annotation, 3.1.6
pro crystallographic tools, 3.2.6
cluster apf, 13.1.9.5
get started, 3.2.1
columns, 12.4.3.1
graphics, 3.2.2
export, 12.4.4
plots, 3.2.8
sequence analysis, 3.2.7
structure analysis, 3.2.3
introduction, 9.1.1
superimpose, 3.2.5
older versions, 9.1.1.3
surfaces, 3.2.4
hover, 17.4.26
selections, 3.1.3
3D editor, 21.7
superimpose, 3.1.8
add columns, 10.3.4
search, 4.2
cluster center, 10.28.2
use gui, 4.1
color 2D by ph4, 10.5.6.5
hrydrogen.bond, 22.2.29
copy 2D, 10.3.16
paste, 10.3.6
html-doc font size, 22.2.1
decompose, 21.6.9
duplicate chemicals, 10.3.21
edit table, 10.3.17
atom display, 16.3.3
tree, 10.28.4
excel, 10.3.10
acceptors, 22.8.17
extract 3D ph4, 10.5.6.4
donor, 10.38.1
filter, 10.3.12
label edit, 5.2.3.1
find replace, 10.3.13
move, 5.2.3.2
mark row, 10.3.14
markush, 21.6.8
structure, 21.6.7
hydrogens, 10.3.28
merge tables, 10.3.23
remove, 10.3.18
properties, 10.3.19
reactions, 21.6.10
hyrophobic, 10.38.1
reorder, 10.28.3
sdf, 10.3.9
show hide, 10.3.8
icm, 22.3.3
sort column, 10.3.5
chemist howto chemical search, 3.4.3
standardize, 10.3.18
cluster, 3.4.5
table hyperlinks, 10.3.15
combi library, 3.4.7
print, 10.3.11
ph4, 3.4.4
activeicm, 3.3
plots, 3.4.8
create molecular documents, 3.3.3
sketch, 3.4.1
slides, 3.3.2
spreadsheets, 3.4.2
getting started, 3.3.1
stereoisomers tautomers, 3.4.6
ppt, 3.3.4
pro 3D ligand editor, 3.5.1
chemsuper, 3.5.4
loaded ligand, 12.3.1.2
energy, 3.5.3
loop, 9.1.4.2
qsar, 3.5.5
modeling, 9.1.4
tutorials, 3.5
table ligand, 12.3.1.1
tutorials, 3.4
modeling, 9.1.4
hanging, 22.1.13
interface prediction, 21.10
internal hydrogen bonds, 12.1.5
script, 17.1.40
internet explorer, 22.3
icm-crash, 22.1.13
interrupt, 6.10.7.3
icmFastAlignment, 8.4
animation, 6.10.7.3
introduction, 1
icmdb, 19
invert selection, 17.1.23
icmjs, 7.16
invisible residue label, 22.1.12
icmpocketfinder, 21.3.7
iqr, 17.4.23
id, 17.1.27
isee, 7.6.5
identity, 4.2.1.2
isis, 10.4.18
isostere, 13.4
advanced, 6.15.3
distortion, 22.1.20
preferences, 4.7.6
javascript, 7.16
problem, 22.1.20
job, 22.5.19
multiple, 3.6.1.7
join, 10.32
quality, 3.6.3.11
jpg, 6.15
means, 17.7.1
images, 6.15
impose, 12.6.2
keep carboxyls neutral, 12.2.1.3
in-a-window, 22.1.7
kernel regression, 15.3.1
inchi, 10.20.3
chemical, 10.4.10
increment, 17.1.27
keyboard mouse, 6.11
id, 17.1.27
keystokes in chem-edit, 10.4.10
index, 22.9.6
models, 15.1.2
knime, 20
induced, 22.5.15
atoms, 6.8.2
insert, 7.6.4
color, 6.8.7
column, 17.1.26
move, 6.8.4
residues, 6.8.3
table, 17.1.34
sites, 6.8.6
row, 17.1.33
variables, 6.8.5
script, 7.6.4
2D, 3.7.3
installation, 22.1
atom, 6.8.1
atoms, 6.8.2
fingerprint, 13.1.9.6
color, 6.8.7
fingerprints, 13.1.9.6
custom, 6.8.8
lists, 13.1.10
restraint, 12.5
distance, 6.8.10
restraints, 12.5
drag, 3.6.3.16
residue, 6.8.1
site, 6.8.1
edit, 16.5
sites, 6.8.6
energy, 16.3
variable, 6.8.1
hydrogen.bond, 16.3
pocket, 16.3
labeling, 6.8.1
preferences, 16.2
restraint, 16.12
distances, 6.8.10
surface, 16.3
tab, 3.7.3
tether, 16.12
landscape, 4.7.6
optimization, 21.11.3
large chemical space, 21.6.4
pocket, 4.1.8
font, 22.1.16
receptor.contact, 5.5.3
size, 22.1.9
ligand_pocket_interactions, 5.2.4
sdf, 10.1.2
ligedit distance restraint, 16.12.2
layer, 6.14
tab, 3.7.5
layers, 6.14
tether, 16.12.1
light, 3.7.2
learning, 11
tab, 3.7.2
theory, 11.5
least.squares, 17.4.16
library, 10.35.4
reaction, 21.6.10
lineWidth, 4.7.3
license, 22.1.4
link, 8.3.9
ligand, 5.2.2, 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
structure to alignment, 21.4
aide, 12.10
linker, 12.14
links, 4.6.20
best replace, 16.6
linux, 10.10.1
binding, 9.16
lipinski rule, 10.34
list, 4.6.18
considerations, 12.1.2
lmhostid, 22.1.18
bioisostere, 16.8
example alignment, 8.3.14
covalent docking, 16.16
nmr model, 4.2.1.4
mrc, 16.15
protein structure, 5.1.1
preferences, 3.6.2.18
sequence, 8.1
energetics, 10.27
extract pdb, 8.1.3
conformational entropy, 10.27.1
from file, 8.1.4
strain, 10.27.2
paste, 8.1.2
swissprot, 8.1.1
surface, 16.3.2
libraries, 9.21.6
receptor contacts, 16.3.12
display, 5.2
databases, 18
interaction, 10.6
database.browse, 18.2
strain, 16.3.10
edit, 18.3
surface, 5.2.2
query, 18.4
tether, 16.12
row, 18.3
localpdb, 22.2.24
convert, 9.21.1
localseq, 22.2.25
binding.re-dock ligand, 16.9
display, 16.3
logD, 10.11.6
logarithmic, 17.4.11
analysis, 10.36.6
logout, 3.6.1.19
materials, 3.7.6
max, 17.7.1
analysis, 9.7
maxColorPotential, 4.7.10
design, 9.4
find pdb segments, 9.7
dendrogram, 10.30.1
tutorial, 21.5.2
rgroup decomposition, 10.28.7
preferred residues, 9.6
measure distance, 22.8.16
model, 9.21.9
to ring, 22.8.16
sample, 9.21.9
energy water, 9.21.17
exposed docking, 12.1.7
font, 22.1.16
memory, 10.1.2
size, 22.1.16
menu, 7.6.5
machine learning, 21.13
chemistry, 3.6.14
macrocycles, 9.20
docking, 3.6.15
macros, 7.14
homology, 3.6.13
molmechanics, 3.6.16
tools chemical search, 3.6.11
alignment, 8.6.1
molecular editor, 3.6.12
animation, 6.10.7.1
windows, 3.6.17
apf docking sar model, 15.6
two sets, 10.32
flat, 22.8.13
mesh, 5.2.1, 5.2.2, 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
molecular document, 7.6
clip, 6.3.10
molt, 18.1
color lighting, 6.3.9.4
receptor maps, 12.2.1.2
options, 6.3.9
selection, 4.6
representation, 6.3.9.3
bond, 22.4.2
save, 6.3.11
options, 6.3.9
molecule, 3.6.1.1
object, 3.6.1.1
surfaces grobs, 6.3
making molecular slides, 7.1
tab, 3.7.6
html, 7.6
metabolic oxidation, 15.7
manual change torsion, 16.5.4
min, 17.7.1
minimization, 9.18
cel, 5.3.5
cartesian, 9.21.8
global, 9.21.8
mark, 17.1.45
local, 9.21.8
row, 17.1.45
minimum specifications, 1
color, 17.4.14
shape, 17.4.13
type, 6.8.2
size, 17.4.13
mmp, 21.6.11
mnSolutions, 4.7.10
docking, 21.11.3
library, 21.6.8
domain interaction, 9.18
mass, 22.4.22
start, 9.1.1.2
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
amino acid, 9.12
editor, 10.4
group, 9.11
moledit, 10.4.8
molmechanics, 22.9.8
minimize, 9.21.8
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
mmff, 9.21.6
add database, 10.10.3
administration, 10.10.5
custom model panel, 15.4
connect, 22.9.2
load models, 15.1.1
download dbs, 22.9.3
run, 15.1
hostid, 22.9.1
model type, 15.3
installation, 10.10.1
results, 15.2
license, 22.1.4
molskin, 6.3.2
search, 10.10.4
molsynth, 10.11.5
start, 10.10.2
connect, 22.9.2
monitor, 22.8.10
hostid, 22.9.1
monochrome, 10.3.28
license, 22.9.1
montecarlo, 22.9.7
molclart, 22.1.4
animations slides, 7
documents, 21.2
column, 17.1.28
mesh, 6.3.9.2
membrane, 14.3
slide, 7.4.2
restraints, 14.2
structure, 6.12
run, 14.1
tools, 6
vls, 14.4
rotate, 6.11
editor, 22.8.2
slab, 6.11
graphics, 6
translate, 6.11
matched pairs, 21.6.11
z-rotation, 6.11
mechanics, 9.21
zoom, 6.11
convert, 9.21.1
design loop, 9.21.10
montecarlo, 22.9.7
edit structure, 9.21.5
gamess, 9.21.16
generate normal mode stack, 9.21.14
mpa, 21.6.11
his asn, 9.21.2
ic table, 9.21.13
impose conformation, 9.21.4
mpo, 10.34
minimize, 9.21.8
binary classification, 10.34.2
mmff, 9.21.6
custom step function, 10.34.1.2
regularization, 9.21.3
customized, 10.34.1
sample loop, 9.21.9
save, 10.34.1.3
peptide, 9.21.12
special cases, 10.34.1.1
multi apf super, 10.37.7
display, 4.2.1.5
panel, 6.2
parameter optimization, 10.34
older version, 3.6.1.10
template, 9.1.4.3
windows, 6.2
online databases, 10.5.5
file, 4.4
position group scan, 16.7
password, 4.4.1
rec, 12.6.2
with password, 3.6.1.4
docking, 16.15
protein, 22.2.5
optimize, 9.21.2
oracle, 19
residue, 22.4.13
orange, 4.6.5
N C, 22.4.14
selection, 4.6.5
protein binding, 9.13
orthosteric, 5.6.6
ligand, 9.16
other selection, 4.6.19
peptide, 9.15
outside, 22.5.9
stability, 9.14
mysql, 19
pH, 10.19
navigate workspace, 4.6.10
package.activeicm, 7.13
nearest, 22.4.22
packing, 5.3.1
pages, 19.7
Torsion Profile Neural Network Prediction Engine, 6.12.6.1
new, 8.1
apf score, 10.38
icm session, 3.6.1.2
parallelization, 13.1.7
table, 17.1.1
password, 10.10.5
table, 17.1.1
nmr, 22.4.18
pca, 17.5
model, 4.2.1.4
nnc, 15.3.5
chem gl, 10.7.3
nntorsion, 6.12.6.1
iw, 10.7.2
nof, 10.11.2
dormat, 4.5
chemical, 10.11.2
file, 22.4.3
non-contiguous selection, 4.6.18
html, 4.2.1.6
normal modes, 9.21.14
preparation, 21.3.11
number of sp3, 10.11.2
numbers, 10.3.28
convert, 9.21.1
nvidia, 22.1.2
recent, 3.6.1.18
obj, 6.7
pdbsearchfield, 3.6.2.13
objects, 5.1.2
pdbsearchhomology, 3.6.2.15
in table, 17.3
pdbsearchidentity, 3.6.2.14
in.table, 17.3
pdbsearcsequence, 3.6.2.16
shading, 6.3.12
docking, 12.12
effect, 6.10.5
modeling, 9.20
editor, 16.20
zoom translate, 17.4.17
ph4, 10.5.6
axis, 17.4.15
draw 2d, 10.5.6.1
display, 17.4.15
3d, 10.5.6.2
grid, 17.4.15
search, 10.5.6.3
inline, 17.4.22
logarithmic, 17.4.12
2D, 21.6.6
3D, 21.6.5
pmf, 22.5.6
clone, 10.5.6.2
draw2D, 10.5.6.1
draw3D, 10.5.6.2
conservation, 22.4.12
properties, 5.8
move, 10.5.6.2
new, 10.5.6.2
peptide, 4.1.8
properties, 4.1.8
phylogenetic, 8.7.8
pockets, 5.6.6
phylogeny, 8.7.8
point label, 17.4.19
physics-based score, 12.4.3.1
portait, 4.7.6
pi, 5.2.5
post edit ligand, 16.5.8
cation, 5.2.5
screen, 13.1.9
pi, 5.2.5
postscript, 4.7.6
picking, 6
potential mean force, 13.1.4
ppbatch, 12.13.9
tips, 4.1.14
ppepitope, 12.13.7
chart, 17.4.8
ppmaps, 12.13.8
pipi, 5.2.5
pprefine, 12.13.11
pka, 10.15
ppresults, 12.13.10
pproc, 12.13.3
angle, 5.5
ppsetligand, 12.13.6
angle, 6.9.2
ppsetproject, 12.13.4
ppsetreceptor, 12.13.5
faq, 22.2.21
plot, 4.7, 4.7.8, 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
R group sar, 10.36.4
disulfide, 9.17
axis, 17.4.11
metabolic oxidation, 15.7
color, 17.4.14
predicting bioassays, 11.2
columns, 17.4.6
compound properties, 11.2
prediction binding, 9.13
grid, 17.4.15
header, 17.4.9
preferred residues, 9.6
inline, 17.4.22
logarithmic, 17.4.12
presentations, 7
mark, 17.4.13
preserve, 22.8.6
mean median iqr, 17.4.23
press-and-hold to rotate, 10.4.8
point label, 17.4.19
pretty view, 16.3.6
preferences, 4.7.8
primary aliphatic amines, 10.15
groups, 17.4.25
principal component analysis, 17.5
regression, 17.4.16
regression, 11
selection, 17.4.18
components, 11.5
alignment, 8.7.4
sites by apf, 5.4.6
plot, 17.4.20
superimpose 3D, 5.4.3
alignment, 8.7.4
grid, 5.4.5
printer.resolution, 4.7.6
multiple proteins, 5.4.4
pro-drug, 10.26
protein-protein, 5.6.5, 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
docking refinement, 12.13.11
problem, 22.1.14
protein-proteindocking, 12.13.7
with selection, 22.1.12
convert, 9.21.1
prodrug, 10.26
protonated, 22.4.15
state, 12.1.4
close, 3.6.1.13
protonation_ph, 10.19
rename, 3.6.1.9
protonation_ph_charge, 10.19.2
protonation_ph_concentration, 10.19.1
protprot, 12.13
expression, 13.1.9.4
monitor, 10.4.9
protac, 12.14
protect, 7.6.8
pubchem, 10.1
publication quality images, 6.3.2
chain, 9.4
pubmed, 4.2.1.7
health, 5.6.3
model, 9.19
pyramid, 12.1.6
protein docking, 21.10
pyramidal, 12.1.6
tutorial, 21.10
qs hydrogen bond, 5.2.3
sculpting, 9.18
pdb chem gl, 5.1.3.2
sequence, 10.4.17
iw, 5.1.3.1
structure, 5
analysis, 5.5
learn predict, 10.21
closed cavities, 5.5.4
predict, 10.22
contact areas, 5.5.3
quad buffer stereo, 22.1
distance, 5.5.6
buffer, 22.1.7
find related chains, 5.5.1
finding dihedral angle, 5.5.8
planar angle, 5.5.7
molt, 18.4
rama export, 5.5.10
processing, 10.5.3
ramachandran plot, 5.5.9
setup, 10.5.1
rmsd, 5.5.2
quick, 4.1.14
surface area, 5.5.5
image, 6.15.2
similarity, 5.7
model multiple chain, 9.1.2.2
tutorials, 21.3
single chain, 9.1.2.1
analysis, 21.3.4
start move structure, 4.1.3
contact area, 21.3.5
read pdb, 4.1.2
convert, 21.3.2
representation, 4.1.6
hydrogen bond, 21.3.6
selection, 4.1.5
icmpocketfinder, 21.3.7
level, 4.6.3
search, 21.3.1
what is selected, 4.6.4
superimpose, 21.3.3
display.distance, 6.9.1
superposition, 5.4
start color, 4.1.7
select, 5.4.1
quit, 3.6.1.19
table, 10.35.2
relaxed ligand, 16.3.9
groups, 10.35.2
dock results, 12.4.5
decomposition, 10.28.7
enumeration, 10.28.7
salt, 22.8.14
r-groups, 17.4.25
explixit.hydrogens, 10.12
salt, 10.12
radar, 17.4.6
rename, 17.1.25
column, 17.1.25
project, 3.6.1.9
range, 6.10.7.2
reorder column, 17.1.29
rapid isostere replacement, 13.4
replace chemical, 10.3.32
ratio.selection, 4.7.5
replacement, 16.6
dock ligand, 16.9
group, 16.8
report, 19.3
reactive cysteine, 5.6.2
representation, 3.6.3.19
reactivity, 10.11.3
alternative orientation, 21.3.11
chemical, 10.1
content, 8.3.1
spreadsheet, 10.3.1
number selection, 22.2.36
split, 11.1.1
range, 4.6.18
table, 17.1.2
pdb, 4.1.2
table, 17
reagent, 10.35.5
mesh, 6.3.9.1
recent files, 3.6.1.17
resolution, 4.2.1.3
pdb codes, 3.6.1.18
receptor, 5.2.1, 5.2.2, 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
default, 22.1.9
considerations, 12.1.1
recent backup, 3.6.2.11
flexibility, 16.15
restrained docking, 12.5
pocket, 16.3.1
restraints, 14.2
flexibility, 21.12.2
results, 12.13.10
recover, 3.6.2.11
stack, 12.4.2
retrieve columns, 22.5.24
from original database, 22.5.24
review and adjust binding site, 12.2.1.1
rgroup, 10.35.4
loops, 9.1.3
side chain, 9.9
as a mesh object, 22.2.3
sidechains, 9.1.3
faq, 22.2.23
refinement, 12.6.4
preferences, 4.7.9
region, 12.13.7
style, 4.7.9
breaks, 6.1.3
regul, 9.8
cylinders, 6.1.3
smooth, 6.1.3
worm, 6.1.3
covalent geometry, 12.2.1.3
ribbonColorStyle, 4.7.9
gpu benchmark, 13.4.1.2
PDB, 4.5
server setup, 13.4.1.1
pdb, 4.5
setup, 13.4.1
chemical mol, 10.4.13
ridge, 13.5
spreadsheet workspace, 10.2.1
right, 4.1.12
to chemical spreadsheet, 10.4.14
click, 4.1.12
docked ligand, 16.19
rigid, 10.37
file, 4.5
substructure superposition to template, 10.37.2
hits, 16.5.7
image plot, 17.4.21
stacking, 5.2.5
ligand receptor complex, 16.19
object, 4.1.9
pdb, 4.5
project icb, 4.1.10
speed, 6.10.7.2
sequence, 8.1.5
root, 22.4.7
slide, 7.4
mean square deviation, 5.5.2
smiles string, 10.4.15
table, 17.1.21
chemical, 10.3.34
spreadsheet, 16.5.7
torsion, 6.12.6.1
tree, 17.7.3
when pasting, 10.4.8
sdf, 10.4.14
easy, 3.6.3.12
speed, 6.10.7.2
object, 4.1.9
rotating fragment in editor, 10.4.8
password, 3.6.1.11
rotation, 6.12.1
picture, 3.6.1.15
rough surface, 22.2.37
table.view, 17.1.8
flag, 17.1.13
saving, 3.6.1.8
project, 3.6.1.8
mark, 17.1.13
scaffold, 10.14
hide, 10.3.8
hopping, 16.8
show, 10.3.8
ruler, 6.8.16
molscreen, 15.1.3
hits, 12.4.1
rundock, 22.5.16
group, 16.7
rxn, 10.4.13
scan_pockets, 5.8
safari, 22.3
scarab, 19
sali, 10.36.5
add user, 19.5
bridge, 21.3.6
browse export data, 19.4
salts, 10.3.18
installation, 19.1
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
atom, 3.6.2.5
sculpting, 9.18
basic, 4.6.2
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
change, 4.6.7
clear, 3.6.2.7
chembl, 4.2.3
column, 17.1.23
drugbank, 4.2.8
filter, 10.5.2
graphical, 4.6.16
in workspace, 3.6.2.4
pdb, 4.2.1
level, 3.6.3.3
chemical, 4.2.1
mode, 3.6.3.4
ligand code, 4.2.7
near atoms, 3.6.2.8
pocketome, 4.2.2
pubchem, 4.2.9
object, 4.6.11
surechembl, 4.2.4
other, 4.6.19
tab field, 4.2.1.3
properties, 3.6.2.5
pdb chemical, 4.2.1.1
range, 17.1.23
sequence, 4.2.1.2
residue, 3.6.2.5
tautomer, 10.5.3
row, 17.1.23
uniprot, 4.2.6
sphere, 4.6.15
in.workspace, 3.6.2.4
spherical, 3.6.2.8
secondary aliphatic amines, 10.15
superposition, 5.4.1
elements, 17.1.23
a tree branch, 17.7.2
whole, 4.6.11
all, 4.6.14
amino acid, 4.6.13
selectioninvert, 3.6.2.6
duplicates, 10.33
selections, 4.6
molecule, 4.6.12
links, 8.3.9
neighbors, 4.6.15
selectneighbors workspace, 4.6.17
graphic, 4.6.16
organized network, 10.30
object, 4.6.11
sequence, 3.6.4, 4.2, 4.2.1.2, 4.2.5, 4.2.6, 4.3, 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
analysis, 8.3
by number, 4.6.18
editor, 8.5
number, 4.6.18
identity, 8.7.15
tree, 17.7.2
pattern, 4.2.1.2
reordering, 8.7.8
similarity, 8.7.15
purple.box, 3.6.3.23
sites, 8.5
structure, 8.3.6
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
extract, 8.3.13
markush, 10.35.1
unique, 8.3.13
reaction, 12.8.1
server, 13.1.7.2
smiles, 10.4.12
error, 22.1.17
formal charges, 10.15
server, 22.1.17
slice, 6.13
bond type, 9.21.5
charges, 9.21.6
effects, 7.5
chirality, 9.21.5
movie, 6.16.1
file, 7.2
bond, 9.21.5
navigation, 7.3.2
formal charge, 9.21.5
show, 7.3
tether, 9.21.5
blend, 7.5
types, 9.21.6
edit, 7.4.1
setAPFparams, 22.8.12
effect, 7.5
setup, 12.13.6
smooth, 7.5
ligand receptor, 16.1
transition, 7.5
alignment, 21.4.4
shading, 6.3.12
smooth, 6.3.9.3
shadow, 6.10.2
surface, 22.2.37
share model, 11.1.5
solid, 6.3.9.3
sheet, 22.2.20
solvent.accessible.area, 22.4.19
shell preferences, 4.7.10
sort hitlist, 13.1.9.1
shift, 6.8.3
table, 3.6.10.4
sorting, 13.1.9.1
shineStyle, 4.7.3
compounds, 17.7
sp3, 10.11.2
hide column, 17.1.39
spec, 3.7.2
side, 10.3.29
specifications, 22.1.5
by side, 10.3.29
specs, 1
error, 22.1.19
faq, 22.1.5
stereo, 3.6.3.6
speed, 6.10.7.2
chain refinement, 16.14
sphere, 22.4.11
chains, 9.9
side-by-side, 22.1.19
split, 10.36.1
side-chain sampling, 12.13.11
spreadsheet, 10.20.2
side-chains, 12.6.1
square, 22.4.7
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, 5.2.3.1
startup, 22.10.2
sketch accents, 6.10.3
static, 22.4.8
bond, 10.4.2
alignment, 17.1.12
hardware, 3.6.3.7
clone, 17.1.16
side-by-side, 3.6.3.6
color, 17.1.10
stereohard faq, 22.1.6
column format, 17.1.40
stereoisomer, 10.20.5
stereoisomers, 10.25
delete, 17.1.17
stick, 4.7.5
edit, 17.1.24
stl, 6.7
filter, 17.1.43
stop, 6.10.7.3
find, 17.1.9
replace, 10.3.32
current view, 3.6.3.19
font, 17.1.11
faq, 22.2.22
size, 22.2.1
grid, 17.1.5
strip, 22.4.9
histogram, 17.4.1
insert, 17.1.26
analysis, 21.3.4
layout, 17.1.5
ensemble, 9.21.14
learning, 17.6
representation, 6.1
mark, 17.1.13
smiles, 10.20.4
row, 17.1.13
structure-based, 13
mouse, 17.1.47
navigation, 17.1.4
style, 4.7.5
new column, 17.1.26
plot, 17.4
print, 17.1.19
template, 16.12.3
rename, 17.1.15
alerts, 10.13
rightclick, 17.1.14
sulfur, 9.10
row height, 22.2.39
save, 17.1.3
3D, 5.4.3
selection, 17.1.3
Calpha, 5.4.3
search, 17.1.9
arrange.grid, 5.4.5
select, 17.1.23
backbone, 5.4.3
setup, 17.1.18
heavy atoms, 5.4.3
sort, 17.1.42
multiple, 5.4.4
split fragments, 10.3.33
view, 17.1.5
save, 17.1.8
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, 10.11.5
compare, 10.3.22
synthetic feasibility, 10.11.5
copy, 10.3.6
system preferences, 4.7.11
cursor, 17.1.47
pdb, 3.7.4
display, 22.10.4
table, 4.3, 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
search, 10.5.4
texture, 3.7.6
find-replace, 10.3.13
to screen, 17.1.4
font, 17.1.11
threshold, 4.7.5
foreground, 22.10.4
tier, 4.1.13
grid lines, 17.1.4
time, 22.5.11
hide, 17.1.39
machine, 22.1.15
hyperlink, 10.3.15
tissue, 4.2.10
insert, 17.1.33
racemic, 10.20
join, 3.6.10.5
tools 3D, 3.6.6
label, 10.3.14
analysis, 3.6.7
landscape, 17.1.18
append rows, 3.6.10.7
mark, 10.3.14
extras, 3.6.9
plot function, 3.6.9.1
mouse, 17.1.47
superimpose, 3.6.8
name, 17.1.15
table, 3.6.10
new, 17.1.1
Learn, 3.6.10.1
options, 17.1.14
clustering, 3.6.10.3
orientation, 17.1.18
merge, 3.6.10.5
portrait, 17.1.18
predict, 3.6.10.2
tooltip, 17.4.26
read, 17.1.2
balloons, 17.4.26
rename, 17.1.15
right click, 17.1.14
analysis, 10.16
row, 17.1.33
rows, 3.6.10.7
free strain, 10.17
scan, 9.21.7
scale, 17.1.18
toxscore, 10.11.3
scroll, 17.1.4
trace, 6.1.10
sdf, 10.3.9
transition.blend, 22.2.31
select, 17.1.23
setup, 17.1.18
standard, 17.1
transparent, 6.3.9.3
view, 10.3.29
background, 6.15.3
width, 17.1.4
ribbon, 22.2.3
surface, 22.2.37
tags, 4.6.21
branch swapping, 8.7.8
distance, 10.28.3
tautomers, 10.24
edit, 10.28.4
temperature, 5.6.4
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
symmetry, 21.3.9
color background, 3.6.3.18
multiple receptor, 21.12.1
dock results, 12.4
tut3, 21.5
fog, 3.6.3.5
tut3e, 21.3.12
macroshape, 3.6.3.22
tut5a, 21.9.1
menu, 3.6.3
tut5b, 21.9.2
mesh clip, 6.13.1
tut5c, 21.11.1
perspective, 3.6.3.9
tut5e, 21.11.2
selection level, 3.6.3.3
tutorial 2D pharmacophore, 21.6.6
mode, 3.6.3.4
3D pharmacophore, 21.6.5
shadow, 3.6.3.13
chemical clustering, 21.6.3
sketch accents, 3.6.3.14
search, 21.6.2
slide show, 7.3.1
molecular documents, 21.2
tools, 3.6.3
sequence alignment, 21.4
tree, 17.7.4
link, 21.4.2
undisplay all, 3.6.3.1
load sequence, 21.4.1
stach, 9.21.15
sequence conservation, 21.4.3
tutorials, 21
ligand screening, 15
ubuntu, 22.1.18
ultra large library, 13.5
examples, 21.11
virus, 5.3.3
visualize, 10.30
box shade font, 8.7.7.1
apf fields, 16.3.11
undisplay-all, 3.6.3.1
chemical space, 10.30
origin, 6.8.12
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
redo, 16.5.5
analysis, 13.1.9.4
display, 13.1.9.3
command line, 13.1.7.2
unit, 5.3.3
getting started, 13.1.2
units, 22.5.1
histogram scatter plot, 13.1.9.2
unix, 22.10.2
introduction, 13.1.1
unsatisfied hydrogen bonds, 16.3.8
preferences, 13.1.4
unusual peptide, 4.3
results, 13.1.8
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, 4.1.13
wireBondSeparation, 4.7.1
working directory, 22.5.23
panel, 4.1.4
selection, 4.6.9
navigation, 4.6.10
alignment, 8.7.3
excel, 10.2.3
images, 6.15
pdb, 4.5
image, 3.6.1.15
object, 4.1.9
picture, 3.6.1.15
table, 17.1.3
writing a pdb file, 22.4.3
ray, 3.6.5
xls, 10.2.3
xlsx, 10.2.3
xml, 19.2
xyz, 22.2.10
youtube, 2