ICM User's Guide: Index

2D, 6.8.8, 10.3.24, 10.3.28, 10.14, 10.20.2, 10.20.4

Baell, 10.4.9

Chemical Label, 6.8.11

Beep, 4.20.11

Interaction Diagram, 16.3.7

Beta-Catenin, 16.20

bioisostere, 10.9.1

Bioactive Conformation, 16.20

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

to 3D, 10.20, 10.20.3

C2′-endo pucker, 5.5.12

depiction, 10.20.2

C3′-endo pucker, 5.5.12

3D, 6.6, 6.8.8, 10.1.3, 10.3.24, 10.3.28, 10.3.31, 10.20.2, 21.2

CHEMRIYA, 13.5

QSAR, 10.38.4, 11.4, 21.14

COLLADA, 3.6.1.7

chemical, 10.4.16, 10.20.1

CPK, 3.7.1

interactive ligand editor, 3.7.5

ChEMBL, 4.16.2, 10.1

ligand editor, 16.3.4

Chemical Cluster, 21.6.3

object, 6.3.9

Search, 21.6.2

pharmacophore, 13.3, 16.3.11

CisTransAmide Angle, 13.1.9.4

print, 6.7

Clash Threshold, 4.20.10

printing, 6.7

Computational Chemistry, 16.20

screening, 15

Computer-Aided Drug Discovery (CADD), 16.20

stereo, 6.6

Covalent Geometry., 16.20

visualization, 5.5.11

DNA, 4.17, 8, 8.3.3

3DMOLT, 18.5

Decomposition, 10.36.3

3DQsar, 11.4

Design Evolution, 12.10

3D_Similarity_PDB_Search, 5.7

Dimer, 5.5.11

3Dqsar tutorial, 21.14

Display, 22.2.26

bioisostere, 10.9.2

Distance, 13.1.9.4

predict, 5.6

Dock Directory, 4.20.2

helices strands, 5.6.1

Docking, 22.2.26

local flexibility, 5.6.4

Drug Bank, 4.16.7

protein health, 5.6.3

Design, 16.20

tools identify ligand binding pocket, 5.6.6

Editor, 4.20.2

oda, 5.6.5

Eintl, 12.1.10

4D, 12.6.2, 21.12.1

Error in saving configuration settings: You are not a license administrator, 22.1.10

dock, 16.15

Extended Amino Acids, 16.20

docking, 4.16.1

FILTER.Z, 4.20.2

64, 22.1.3

gz, 4.20.2

A-form RNA, 5.5.12

uue, 4.20.2

AI, 12.10

FTP.createFile, 4.20.11

APF, 10.37.4, 10.37.7, 10.38.4, 11.4, 15, 15.6, 21.14

keep File, 4.20.11

template, 10.37.3

proxy, 4.20.11

Acetyl Cap, 16.20

Filter.zip, 4.20.2

ActiveICM, 3.6.1.12

Flexible Minimization, 16.20

Alignment mode, 5.5.11

Force Auto Bond Typing, 4.20.11

Alpha-Helix Stabilization, 16.20

Formula, 22.8.7, 22.8.10

Altona-Sundaralingam pseudorotation, 5.5.12

Free Wilson, 10.36.2

Area, 9.21.18, 22.2.26

Frequently Asked Questions, 22

Atom Single Style, 4.20.3

GAMESS, 9.21.16

Atomic Property Fields, 11.4, 21.14

GIF, 3.6.1.15, 6.16, 6.16.2

Bad Groups, 22.8.7, 22.8.10

GINGER, 10.23

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

HBA, 13.1.10, 22.8.7, 22.8.10

light, 4.20.3

HBD, 13.1.10, 22.8.7, 22.8.10

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, 16.20

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, 16.20

Range, 4.20.4

Hydrogen.bond, 4.20.5

Speed, 4.20.4

I+4 Staple Position, 16.20

selectionStyle, 4.20.3

Staple Position, 16.20

site Label Drag, 4.20.7

ICM Browser How To, 3.1

analysis tools, 5.5.12

Markush, 21.6.9

graphics crash, 22.1.11

create, 21.6.7

start, 1

File Size Mb, 4.20.11

ICM-Pro Tutorial, 16.20

Max_Fused_Rings, 10.11

IMAGE.bondLength2D, 4.20.6

Mnconf, 4.20.10

color, 4.20.6

Model, 11.4

compress, 4.20.6

MolCart, 22.9

gammaCorrection, 4.20.6

MolIPSA, 22.8.7, 22.8.10

generateAlpha, 4.20.6

MolLogP, 22.8.7, 22.8.10

lineWidth, 4.20.6

MolLogS, 22.8.7, 22.8.10

lineWidth2D, 4.20.6

MolPSA, 10.11

orientation, 4.20.6

MolScreen, 15

paper Size, 4.20.6

MolSoft ICM-Pro, 16.20

previewResolution, 4.20.6

MolVol, 10.11

previewer, 4.20.6

Molcart, 10.5.3

print, 4.20.6

MoldHf, 10.11, 22.8.7, 22.8.10

printerDPI, 4.20.6

Molecular Docking, 16.20

scale, 4.20.6

Dynamics, 14.5

stereoAngle, 4.20.6

Preparation, 16.20

stereoBase, 4.20.6

Movie.fade Nof Frames, 4.20.4

stereoText, 4.20.6

quality, 4.20.4

INCHI, 10.20.3

Auto, 4.20.4

IQR, 17.4.6

Multimer, 5.5.11

ISIS, 22.8.3

NCBI, 22.2.25

Icm Prompt, 4.20.10

NH2 Cap, 16.20

InChi, 10.3.20, 10.4.12, 10.20.3

NVIDIA, 22.1

key, 10.3.20

Natural Amino Acids, 16.20

Interaction Diagram 2D, 16.3.7

Nof_Atoms, 10.11

Interactive Ligand Editor, 16.20

Nof_Chirals, 10.11

Plot, 5.5.12

Nof_HBA, 10.11

Internal Coordinates Table, 9.21.13

Nof_HBD, 10.11

Directory, 4.20.2

Nof_Rings, 10.11

JPEG, 3.6.1.15

Nof_RotBonds, 10.11

KMZ, 3.6.1.7

Non-overlap, 13.1.9.4

LCC, 13.5

North conformation, 5.5.12

LigStrain, 16.20

Nvidia GL failutre, 22.1.11

Ligand Strain, 16.20

ODA, 22.2.26

Log Directory, 4.20.2

Optimal, 22.2.26

LogP, 11, 17.6

Output Directory, 4.20.2

LogS, 11, 17.6

PAINS, 10.4.9, 10.11.3

MD, 14, 14.1, 14.2, 14.3, 14.4, 14.5

chemicals, 10.4.9

Q&A, 14.5

PCA, 11.1, 11.5, 21.6.4

MOL, 10, 10.3.3, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 13.1.3, 17.2

analysis, 10.29

MOL2, 13.1.3

PDB, 4.2.7, 5.1.2, 5.3.3, 5.7, 8.1, 10.1.1, 16.19

MOLT, 18.1

7UWI, 16.20

MOVIE.frame Grab Mode, 4.20.4

Directory, 4.20.2

MPO, 10.34

Style, 4.20.2

Mac, 22.1.15

link, 17.1.40

Atom Margin, 4.20.10

Search, 3.6.2.12, 3.6.2.13, 3.6.2.14, 3.6.2.15, 3.6.2.16

Sigma Level, 4.20.10

Field, 3.6.2.13

Identity, 3.6.2.14

RNA, 4.17

Sequence, 3.6.2.16

backbone conformation, 5.5.12

convert, 5.1.2

chain analysis, 5.5.12

PFAM, 3.6.1.7

conformation, 5.5.12

PLOT.Yratio, 4.20.8

pucker, 5.5.12

color, 4.20.8

structure analysis, 5.5.12

date, 4.20.8

sugar conformation, 5.5.12

draw Tics, 4.20.8

RTCNN, 12.1.9, 12.4.3.1

font, 4.20.8

Score, 16.20

fontSize, 4.20.8

Ramachandran Plot, 5.5.9

labelFont, 4.20.8

Real Format, 4.20.10

lineWidth, 4.20.8

Reinforce Helix Tool, 16.20

logo, 4.20.8

Relax Geometry Command, 16.20

markSize, 4.20.8

Label Shift, 4.20.7

orientation, 4.20.8

Style, 4.20.7

paper Size, 4.20.8

Residue Replacement, 16.20

previewer, 4.20.8

RotB, 22.8.7, 22.8.10

rainbowStyle, 4.20.8

Rotation angle, 5.5.11

seriesLabels, 4.20.8

Rotational symmetry axis, 5.5.11

PLS, 11.1

SALI, 10.36.5, 21.6.11

PNG, 3.6.1.15, 4.15, 6.16, 6.16.2

SAR, 11, 15.6, 17.4.25, 17.6

PROTAC, 12.14

table, 10.36.3, 21.6.9

PSA, 10.11.7

SCARE, 12.6.4

Peptide Engineering, 16.20

SCORE, 22.5.6, 22.5.17

Mode, 16.20

SDF, 10, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 13.1.3, 17.2

Modeling, 16.20

SEQUENCE.site Colors, 4.20.4

Stapling, 16.20

SITE.label Style, 4.20.7

Pharmacophore RMSD, 13.1.9.4

labelOffset, 4.20.7

PowerPoint, 21.2, 22.3

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

SMILES, 10.1.2, 10.2.4, 10.4.12

complex, 5.5.11

Score, 12.1.9, 12.4.3.1

Protein-Peptide Interactions, 16.20

Select Min Grad, 4.20.10

Viewer, 4.20.2

Sequence Editing, 16.20

Pseudorotation Interactive Plot, 5.5.12

Show Res Code In Selection, 4.20.7

Pub Chem, 4.16.8

Sidechain Optimization, 16.20

PubMed Reference, 17.1.40

Smiles, 22.8.7, 22.8.10, 22.8.11

Pubchem, 4.16.8

South conformation, 5.5.12

QSAR, 11, 11.1, 17.6, 21.14

Special Cases, 10.34.1.1

R, 10.8, 10.36.1

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

REAL, 10.5.5, 13.5

Swissprot, 3.6.1.7

RIDE, 18.5

Dat, 4.20.2

RIDGE, 18.5

link, 17.1.40

- Rapid Docking GPU Engine, 13.5

Symmetry, 5.5.11

RMSD, 5.4.2, 9.21.18

Temp Directory, 4.20.2

RMSF, 9.21.18

Terminal Capping, 16.20

Torsion Minimization, 16.20

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

sequence, 8.6, 8.6.6

organization, 4.20.11

two sequences, 8.3.5, 8.6.2

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

VLS, 13.1, 13.1.1, 13.1.2, 13.1.9.2

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

Volume, 22.8.7, 22.8.10

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

structure, 8.7.16, 22.6.2

a-bright, 3.7.2

selection, 8.7.13

about model, 11.1.3

strength, 8.3.8

acceptor, 10.4.9, 10.38.1

profile, 8.3.8

active, 7.7, 22.3.3

view options, 8.7.10

activeICM, 7.8

color, 8.7.9

activeicm, 7.7, 7.12, 7.14, 7.14.1, 22.3

comment, 8.7.6

advanced, 7.14

consensus, 8.7.9, 8.7.14

background images, 7.15

cut, 8.3.11

control, 7.13

display title, 8.7.10

activeicmjs, 7.16

editor, 8.7

activity, 11, 17.6

extract, 8.3.10

cliff, 10.36.5, 10.36.6, 21.6.11

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

multiple, 8.3.7, 8.6.5

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

selection, 8.7.13, 8.7.14

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

alignments, 8.6, 21.4

align, 4.12, 10.14

allosteric, 5.6.6

color 2D scaffold, 10.14

alpha, 3.7.2

dna protein, 8.6.4

channel, 4.20.6

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

anaglyph, 6.6, 22.1, 22.1.8

2D coordinates, 10.20.2

stereo faq, 22.1.8

helices, 5.6.1

analysis, 3.6.4, 8.3

strands, 5.6.1

angle, 5.5.7, 5.5.8, 6.8.5, 6.9, 6.12.6, 10.16, 22.2.18, 22.4.16

atom, 4.20.5, 10.3.28, 22.2.4, 22.2.5, 22.2.8, 22.2.16, 22.2.17, 22.4.10

angstrom, 22.4.7

charge, 22.4.21

animate, 3.6.3.15, 6.10.7

atomLabelStyle, 4.20.7

view, 6.10.7

atomic energy circles, 16.3.5

animation, 6.10.7.1, 6.10.7.2, 6.10.7.3, 6.10.7.4

property field, 10.37.5, 10.37.6, 16.3.11

store, 6.10.7.4

score, 10.38.2

animations, 7

fields, 5.4.6, 5.8, 10.38, 10.38.1, 10.38.3, 13, 21.8

annotate, 4.6.21, 10.13

attachment, 10.4.3, 10.5.1

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

antialias, 3.6.1.15, 3.6.3.10

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

avi, 6.16, 6.16.2

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

b-factor, 5.6.4, 21.3.10

screen, 10.38.3

coloring scale, 22.2.38

tutorial, 21.8

backbone, 6.1.10, 22.2.13

cluster, 21.8.5

background, 6.4.2, 6.4.3

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

applying prediction models, 11.2

basicsel, 4.6.2

area, 5.5.3, 5.6.5, 12.13, 12.13.2, 12.13.3, 21.3.5

batch, 12.3.2, 12.13.9

aromatic, 10.3.28, 10.38.1

file, 12.3.2.2

arrange, 4.14.1

index, 12.3.2.4

window, 4.14.1

loaded icm object, 12.3.2.1

molcart, 12.3.2.5

calculate, 10.11, 22.5.2

run, 12.3.3

properties, 10.11

bayesian classifier, 11

sequence similarity, 8.7.15

bbb, 10.11.4

startup, 22.10.2

beep, 22.2.35

carbon, 22.2.4, 22.2.5

begin docking simulation, 12.3

carboxylic acid, 10.15

best, 10.3.34

cartesian, 10.23

bicyclics, 10.4.6

cation, 5.2.5

binding, 21.5.3, 22.2.14, 22.5.2, 22.5.10

cavities, 5.5

properties, 6.3.1

closed, 5.5.4

bioinfo align multiple, 8.3.7

ccp4, 22.2.27, 22.2.28

two sequences, 8.3.5

cell, 5.3.2

links, 8.3.9

center, 3.6.3.20, 4.4, 6.12, 6.12.5, 16.3.13, 17.1.40, 22.4.22

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

bioisostere, 10.9, 10.9.1, 10.9.2, 16.8

chair, 22.5.20

biological, 5.3.3

change box size, 16.9.1

biomolecule, 3.6.5, 5.3.3, 21.3.8, 21.3.12

height of all rows, 17.1.7

bit, 22.1.3

ligand, 16.5.1

blast, 4.16.4, 8.4

residue number, 9.2

search, 4.16.4

row height, 17.1.7

blood brain barrier, 10.11.4

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

bond, 5.1.3, 5.2.4, 5.2.4.1, 5.2.4.2, 9.10, 10.4.10, 22.4.1, 22.8.7, 22.8.10

groups, 12.2.1.3, 22.5.22

covalent, 22.4.2

check box, 7.6.6

type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3

convert, 22.8.5

bonding, 6.1.8

export excel, 10.2.3

preferences, 4.20.1

save, 10.2

box, 4.20.7, 6.8.16, 8.7.7, 8.7.7.1, 22.5.9

3D, 10.2.5

alignment, 21.4.4

editor, 10.2.4

size, 16.9.1

image, 10.2.6

browse, 10.3.31, 12.4.1, 19.4

table, 10.2.2

mode, 10.3.31

super, 10.37

molt, 18.2

view, 10.3.28

stack, 9.21.15

chembl, 4.16.2, 4.16.3

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

clustering, 10.28, 10.28.6

homology model, 9.1.2

descriptors, 22.8.15

hydrogens, 9.21.5

dictionary, 10.4.4, 10.4.5, 10.4.6

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

editor, 10.4, 10.4.8

trace, 6.1.10

not starting, 22.1.13

ca-trace, 6.1.10

fingerprint, 15

cache, 7.14.1

fingerprints, 22.8.15

group, 10.4.5

remove.redundant, 10.33

groups, 10.4.5, 10.4.8

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

search, 10.5, 13.4

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

spreadsheet, 4.16.2, 10.1.3, 10.3.1, 10.4.14, 21.6.1, 22.8.13

select, 21.6.4.2

compare, 10.3.22

chi, 6.8.5, 22.2.18

template, 10.3.2

chimeric ligands, 12.9

spreadsheets, 10.3

chiral, 10.25, 12.1.3

substituent, 10.9

chirality, 10.25, 12.1.3

substructure, 4.2.2

considerations, 12.1.3

table, 16.10, 22.8.11

chrome, 22.3

display, 10.3.3

cis trans proline, 21.5.2

tables, 17.2

clash, 4.20.5, 6.8.15

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

clustering, 10.28, 10.28.1

selection, 4.6.6

convert, 5.1.3, 5.1.3.1, 5.1.3.2, 9.21.1, 10.7, 10.7.1, 10.7.2, 10.7.3, 22.4.1

planes, 3.6.3.2

display.fit, 22.8.13

click, 4.13, 6.11, 6.12

draw, 10.4.1

clip, 6.3.10, 6.13.1, 22.2.11

duplicates, 10.3.21

clipboard, 6.15.3, 17.7.3

editor, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6

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

query, 10.4.3, 10.5.1, 10.5.3

close, 6.3.3, 6.3.4, 16.22

read, 10.1

downstream cluster, 10.28.5

save, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13

project, 16.22

search, 10.4.3, 10.5, 10.5.1, 10.5.3

cavities, 5.6.6

similarity, 10.4.3, 10.5, 10.5.1, 10.5.3

cloud, 13.1.7, 13.1.7.2

spreadsheet, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3

cluster, 9.21.18, 13.1.7, 13.1.9.5, 17.7.1

structure, 10.4.13

stack, 9.21.18

superposition, 10.37.3, 10.37.7

representative.center, 10.28.2

table, 10.3, 17.2

clustering, 17.7, 21.6.3

cheminformatics, 10, 10.3, 22.8

cns, 10.34

tutorials, 21.6

collada, 3.7.6, 6.3.7

chemistry, 10.24, 22.8

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

key, 22.2.38

consensus, 10.38, 21.8.2

scale, 22.2.38

pharmacophore, 10.38.1

surface by proximity, 6.3.3

construct, 3.6.1.1, 6.10.7.1

selection, 6.3.4

molecule, 3.6.1.1

table, 10.3.27

object, 3.6.1.1

2D sketch, 10.5.6.5

contact, 5.5, 5.5.3, 21.3.5

background, 3.6.3.18, 6.4.2

surface, 6.3.2

distance, 6.8.10

contacts, 6.3.3, 6.3.4, 10.6, 13.1.9.6, 16.3.12

mesh, 6.3.9.3

contour, 5.3.6, 5.3.7

table, 10.3.27

convert, 5.1.2, 10.20.1, 10.20.5, 22.8.5

coloring, 6.4.1

chemical, 10.3.24

column, 17, 17.1.6, 17.1.22, 17.1.25, 17.1.39, 17.1.40, 17.4, 17.4.1, 22.8.7

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

pdb, 5.1.2, 21.3.2

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

smiles, 10.20, 10.20.3, 10.20.4

show, 10.3.8

coordinates, 10.1.3

combinatorial chemistry, 10.35

copy, 10.3.25, 10.4.11, 10.4.18, 10.5.6.2, 17.1.35

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

compare, 10.3.29, 10.31, 10.32

covalent, 16.10.1

table, 10.3.22

bond, 5.6.2, 21.9.3

tables, 10.31

docking, 12.8, 12.8.1, 16.16, 21.9.3

compatible, 3.6.1.10

tutorial, 21.9.3

complex, 10.6, 13.1.9.3

cpk, 6.1.5, 22.2.21

compound, 4.2.4, 10.24, 17.2

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, 5.6.6

conformation, 9.21.18, 10.23, 12.6.2

crystal, 5.3.2

conformational entropy, 10.27

crystallographic analysis, 5.3

conformations, 22.9.8

biomolecule, 5.3.3

conformers, 10.23

contour map, 5.3.6

connect, 6.3.9.1, 6.12, 6.12.7

convert2grid, 5.3.7

object, 6.12.7

crystallographic cell, 5.3.2

connectivity, 10.4.3, 10.5.1

load eds, 5.3.4

symmetry packing, 5.3.1

depth, 6.3.12, 6.10.5

tools, 21.3.8

deselect, 22.2.7

cell, 3.6.5

design loop, 9.4, 9.21.10

neigbor, 5.3.1

deviation, 22.4.7

neighbors, 3.6.5

dfa, 15.3.3

crystallography, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28

dfz, 15.3.2

csv, 10.2.3, 17.1.2, 17.1.3, 17.1.21, 19.2

dialog, 7.6.5

current, 22.2.22

diffuse, 3.7.2

slide, 7.13

dihedral, 5.5.8, 6.8.5, 22.2.18

curves, 17.4.5

angle, 5.5

custom, 6.12, 10.3.3, 10.37

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, 5.6.2

distance restraints, 6.8.14

cysteine reactivity, 5.6.2

distance2, 6.9.1

damaged skin, 22.1.12

angles, 6.9

dash, 22.2.12

formal charge, 6.1.9

database, 8.4, 10.10, 10.35.4, 13.1.3, 13.1.6, 18.1, 19

gradient, 6.8.17

file format, 13.1.3

hbond, 13.1.9.3

search and alignment, 8.4

hbonds, 13.1.9.4, 16.3.4

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

decomposition, 10.35.4, 10.36.1, 17.4.25

options, 16.3

decoration, 16.18

planar angle, 6.9.2

default, 4.14

tab, 3.7.1, 22.2.16

delete, 3.6.2.1, 4.6.6, 7.6.8, 22.4.9

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

distance, 6.8.10, 6.8.14, 6.9.1

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

density, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28

potential, 3.6.3.21

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

surface, 6.1.6, 6.3.1

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

results, 12.4, 12.4.1, 12.4.2, 12.4.3

xstick, 6.1.2

sampling, 22.5.20

distance, 5.5, 5.5.6, 6.8.10, 6.9, 10.31, 22.2.12, 22.4.8, 22.4.10

score, 12.4.3

faq, 22.4.10

stack, 12.4.2

restraint, 12.5

template, 12.7

label, 4.20.7

document, 7.6.4, 7.6.5

distances, 3.7.3

navigation, 7.6.7

disulfide, 9.10, 9.17

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

download, 22.1.1, 22.9.3

covalent, 16.10.1

dpc, 15.3.4

docked ligand strain, 12.1.10

drag, 4.12, 4.20.7, 6.8.3, 7.6.4, 8.6.6, 22.4.5

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

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

draw, 10.4.18, 10.35.5, 22.8.2

explicit group, 21.12.2

chemical, 10.4.1

from table, 12.3.1.1, 12.3.1.2

drop, 4.12, 7.6.4, 8.6.6, 22.4.5

macrocycles, 12.2.1.3

drug, 10.11, 22.8.7, 22.8.9

maps, 12.2.1.1, 12.2.1.2

bank, 4.16, 4.16.7, 10.1

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, 4.9

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

edit, 5.2.4.1, 16.5.8, 22.8.3

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

ligand, 16.5, 16.5.1

waters, 12.1.8

2D, 16.5.1

background, 22.5.19

editor preferences, 16.2

tools, 3.6.2.17

ensemble, 12.6.2

menu, 3.6.2

calculations, 9.21.18

molecular document, 7.6.1

entropy, 10.17, 10.27.1

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

error, 22.1.3, 22.1.19, 22.2.35

editpdbsearch, 3.6.2.12

evaluate score strain, 16.4

eds, 5.3.4, 5.3.6, 5.3.7

exact, 10.31

effect of mutation, 9.15, 9.16

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

effort, 10.23, 10.37, 22.5.12

explicit, 10.3.28, 12.6.1

electron, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28

flex, 12.6.1

denisty map, 5.3.5

group, 12.6.3

density map, 3.6.1.7, 3.6.5, 5.3.4, 5.3.6, 12.11

docking, 12.6.3

contour, 3.6.5

groups, 21.12.2

electrostatic coloring scale, 22.2.38

export, 5.5.10, 19.4

potential, 3.6.3.21

dock project, 16.21

surface, 6.3

pdb, 4.19

electrostatics, 6.3.1, 12.13.8

extra windows, 6.2

elegant sketch, 6.10.4

extract, 4.18.2, 8.1, 10.1.3, 22.4.12, 22.8.8

element, 10.4.10

2D, 10.1.1

eln, 19.7

3d coordinates to spreadsheet, 10.1.3

embed browser, 7.11

icb, 3.6.1.5

powerpoint03, 7.8

object icb, 4.18.2

powerpoint07, 7.9

sub alignment, 8.3.10

powerpoint10, 7.10

icb, 3.6.1.5

activeicm, 7.13

pharmacophore, 10.5.6.4

script, 7.13

faq, 22, 22.2, 22.2.13, 22.4, 22.5, 22.7, 22.10, 22.10.2

browser, 7.7, 7.11

ISISdraw, 22.8.3

firefox, 7.7, 7.11

MolCart, 22.9

internet.explorer, 7.7, 7.11

activeicm, 22.3

microsoft, 7.7

path, 22.3.3

powerpoint, 7.7, 7.8, 7.9, 7.10

alignment secondary structure, 22.6.2

empty hostid, 22.1.18

apf model, 22.8.12

enamine, 10.5.5

atom charge, 22.4.21

real, 13.5

display, 22.2.17

enantiomer, 22.5.21

autosave, 22.2.33

enantiomers, 12.1.3

backbone, 22.2.13

endocyclic torsion angles, 5.5.12

background color, 22.2.2

energy, 5.6.3, 6.8.15, 10.27, 10.27.2, 12.4.2, 22.5.1, 22.5.2, 22.9.8

job, 22.5.19

circles, 13.1.11

beep, 22.2.35

maps, 12.2.1.1, 12.2.1.2

binding energy, 22.5.2

terms, 9.21.19

blend transition, 22.2.31

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

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

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

front, 6.3.10, 6.13.1

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

function, 17.1.26, 17.1.32

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

filter, 18.2, 22.2.4

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

generator, 5.3.3, 10.23

fingerprint, 11, 11.3, 21.13, 22.8.1, 22.9.5

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

fit, 10.3.34, 12.11, 22.5.15

ginger, 10.23

fitting, 12.11, 17.4.16

glasses, 6.6, 22.1.6, 22.1.14

five-membered ring conformation, 5.5.12

glutamine proline, 9.21.2

flexibility, 5.6.4, 12.6.3, 21.12

google, 3.6.1.7

flexible, 10.37, 12.6, 12.6.1, 12.6.2, 21.12.1, 22.5.15

objects, 6.3.7

APF superposition to template, 10.37.4

3D, 3.7.6, 6.3.7

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

display, 5.1.3.1, 5.1.3.2, 10.7.2, 10.7.3

fog, 3.6.3.5, 6, 6.10.1

tutorial, 21.1

font, 4.20, 4.20.7, 5.2.4.1, 6.8.2, 6.8.3, 8.7.7, 8.7.7.1, 10.3.28, 17.1.40, 17.7.4

2D3D labels, 21.1.4

preferences, 4.20.7

annotation, 21.1.2

size, 8.7, 22.1.16, 22.2.1

color representation, 21.1.1

form view, 17.1.5

labels, 21.1.3

formal, 5.1.3, 22.4.21

user interface, 22.2

charge, 6.1.9, 10.15, 10.18

card, 22.1.2

format, 17.1.2, 17.1.40

controls, 6

formula, 10.4.9, 10.11

defects, 22.1.12

fragment, 10.3.35, 10.36.1, 13, 13.2, 16.11

effects, 6.10

linking, 16.11

panel, 6.2

screening, 13.2

preferences, 4.20.3

fragments, 10.8

shadow, 3.6.3.13, 6.10.2

frame, 8.3.3

green arrows, 8.7.16, 22.6.2

free energy, 9.13, 9.14

lines, 8.2, 22.6.1

radical, 10.4.7

grid, 10.3.3, 10.37, 21.12.1, 22.8.4

wilson regression analysis, 10.36.2

grob, 4.20.5, 5.3.4, 5.3.6, 5.3.7, 6.3

freedomspace, 10.5.5

group, 10.36.1, 16.6

groupGen, 16.18

introduction, 9.1.1

groups, 10.8, 10.11, 10.12

older versions, 9.1.1.3

guanidinium, 10.15

hover, 17.4.26

gui, 4.1, 4.20.4

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

guided docking, 12.5, 22.5.3

copy 2D, 10.3.16

h-bond, 5.2.4, 5.2.4.1, 5.2.4.2, 22.2.12

paste, 10.3.6

halogen, 10.11.2

decompose, 21.6.9

hardware stereo, 3.6.3.7, 22.1

duplicate chemicals, 10.3.21

hba, 13.1.10

edit table, 10.3.17

hbd, 13.1.10

tree, 10.28.4

hbond, 5.2, 21.3.6, 22.2.29

excel, 10.3.10

strength, 22.2.29

extract 3D ph4, 10.5.6.4

header, 4.2.7, 17.4.9

filter, 10.3.12

health, 5.6.3

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

histidine, 9.21.2, 22.4.15

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

hitlist, 12.4, 12.4.3, 13.1.8, 13.1.9.1, 13.1.9.5, 14.4, 22.5.7

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

homology, 4.2.3, 4.16.4, 9, 9.1, 9.1.1, 9.1.1.1, 9.1.2.1, 9.1.2.2, 9.1.3.1, 9.2, 9.3, 9.8, 21.5

sequence analysis, 3.2.7

model, 9.1, 9.1.1.2

structure analysis, 3.2.3

surfaces, 3.2.4

image, 4.15, 4.20, 4.20.5, 6.15.3, 7.6.3, 10.2, 10.2.6, 17.4.21, 22.1.20

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

html, 3.6.1.12, 4.17, 7.6.1, 7.6.7, 22.3

multiple, 3.6.1.7

html-doc font size, 22.2.1

quality, 3.6.3.11

hybridization, 10.4.3, 10.5.1

quick, 3.6.1.14, 6.15.2

hydrogen, 5.2.4, 5.2.4.1, 5.2.4.2, 6.1.8, 10.4.3, 10.5.1, 21.3.6, 22.2.12, 22.8.7, 22.8.10

images, 6.15

atom display, 16.3.3

impose, 12.6.2

bond, 5.2, 6.1.8, 10.6, 13.1.9.3, 21.3.6

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

bonds, 5.2.1, 12.1.5

induced, 22.5.15

bond, 10.4.9, 22.4.20

fit, 12.6, 12.6.1, 12.6.3, 16.13, 21.12, 21.12.1

hydrogens, 10.3.28

insert, 7.6.4

remove, 10.3.18

column, 17.1.26

hyperlink, 7.6.1, 7.6.2, 17.1.40

image, 7.6.3, 17.1.34

hyrophobic, 10.38.1

table, 17.1.34

iSee, 3.6.1.5, 3.6.1.12, 4.11, 6.15.3, 21.2, 22.2.30, 22.2.31, 22.3.3

row, 17.1.33

icb, 4.18.2, 4.19, 22.2.30, 22.3.3

script, 7.6.4

icm, 22.3.3

install, 1, 10.10.1, 19.1, 22.1.3, 22.1.4

chemist howto chemical search, 3.4.3

installation, 22.1

cluster, 3.4.5

interaction, 5.5.3, 10.6, 22.2.12

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

interactions, 16.3.12, 22.5.2

pro 3D ligand editor, 3.5.1

interactive, 12.3.1, 21.2

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

object, 5.1, 21.3.2

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

icmPocketFinder, 5.6.6, 22.2.14, 22.5.10

invert selection, 17.1.23

icmdb, 19

invisible residue label, 22.1.12

icmjs, 7.16

iqr, 17.4.23

icmpocketfinder, 21.3.7

isee, 7.6.5

id, 17.1.27

isis, 10.4.18

identity, 4.2.3

isostere, 13.4

iupac, 10.2.7, 10.3.20

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

kcc, 15.3.1, 15.5

aide, 12.10

keep carboxyls neutral, 12.2.1.3

based screen, 10.38.3, 13.3

kernel regression, 15.3.1

best replace, 16.6

chemical, 10.4.10

binding, 9.16

keyboard mouse, 6.11

code, 4.2.4, 4.16.6

keystokes in chem-edit, 10.4.10

considerations, 12.1.2

kmz, 3.7.6, 6.3.7

editor, 16, 16.10, 16.10.1, 16.16, 16.17

knime, 20

bioisostere, 16.8

label, 4.20.7, 17.7.4, 22.2.17

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

pocket, 5.2.1, 22.4.11

2D, 3.7.3

surface, 16.3.2

3D, 3.7.3, 6.8.1

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

delete, 6.8.1, 6.8.9

tether, 16.12

distance, 6.8.10

ligand-based, 13, 13.3

drag, 3.6.3.16

ligand-induced RNA conformational changes, 5.5.12

move, 3.6.3.16, 6.8.4

convert, 9.21.1

residue, 6.8.1

editor, 16, 16.1

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

variables, 6.8.5, 22.2.18

hydrogen.bond, 16.3

labeling, 6.8.1

pocket, 16.3

labels, 6.8, 10.3.28

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

size, 22.1.9

receptor.contact, 5.5.3

sdf, 10.1.2

ligand_pocket_interactions, 5.2.1

layer, 6.14

ligedit distance restraint, 16.12.2

layers, 6.14

tab, 3.7.5

learn, 10.21, 10.22, 11, 11.1, 17.6, 22.8.12

tether, 16.12.1

learning, 11

light, 3.7.2

lighting, 6.3.9.4, 6.5

font, 22.1.16

likeness, 10.11, 22.8.9

size, 22.1.16

line, 4.20.5, 17.7.4, 22.2.12

machine learning, 21.13

lineWidth, 4.20.3

macrocycles, 9.20

link, 8.3.9

macros, 7.14

structure to alignment, 21.4

macroshape, 3.6.3.22, 6.3, 6.3.6

linker, 12.14

make, 6.10.7.1, 17.1.1

links, 4.6.20

alignment, 8.6.1

linux, 10.10.1

animation, 6.10.7.1

lipinski rule, 10.34

apf docking sar model, 15.6

list, 4.6.18

complex, 13.1.9.4, 16.22

lmhostid, 22.1.18

flat, 22.8.13

load, 3.6.1.3, 3.6.1.17, 5.3.4, 5.3.6, 5.3.7, 8.1

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

disulfide, 9.10, 22.4.17

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

local, 22.2.24, 22.2.25

manual change torsion, 16.5.4

databases, 18

map, 4.20.7, 5.3.4, 5.3.6, 5.3.7

database.browse, 18.2

cel, 5.3.5

edit, 18.3

maps, 12.2.1.1, 12.2.1.2, 12.13.8, 21.12.1, 22.2.27, 22.2.28, 22.5.9

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

lock, 6.3.10, 6.13.1, 10.3.31

size, 17.4.13

log, 17.4.6, 17.4.11

markush, 10.28.7, 10.35.1, 10.35.3, 10.36.1, 21.11.3

logD, 10.11.6

docking, 21.11.3

logP, 10.4.9, 10.11

library, 21.6.8

logS, 10.4.9, 10.11

mass, 22.4.22

logarithmic, 17.4.11

matched pair, 10.36.6, 21.6.11

logout, 3.6.1.19

analysis, 10.36.6

loop, 9.3, 9.5, 22.2.20

materials, 3.7.6

analysis, 9.7

max, 17.7.1

design, 9.4

maxColorPotential, 4.20.10

find pdb segments, 9.7

maximum common substructure, 10.28.6, 10.30, 10.30.1

model, 9.3, 9.4, 21.5.2

dendrogram, 10.30.1

tutorial, 21.5.2

mcs, 10.28.6, 10.30.1

modeling, 9.1.4.2, 9.6, 9.7, 9.21.10

rgroup decomposition, 10.28.7

preferred residues, 9.6

mean, 17.4.6, 17.4.23, 22.4.7

model, 9.21.9

measure distance, 22.8.16

sample, 9.21.9

to ring, 22.8.16

energy water, 9.21.17

median, 17.4.6, 17.4.23

mac, 10.10.1, 22.1.9, 22.1.16

membrane, 12.1.7, 14.3

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

merge, 10.32, 22.4.5

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

molecular, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.23, 22.8.7, 22.8.10

clip, 6.3.10

animations slides, 7

color lighting, 6.3.9.4

documents, 21.2

options, 6.3.9

dynamics, 14, 14.1, 14.2, 14.3, 14.4

representation, 6.3.9.3

membrane, 14.3

save, 6.3.11

restraints, 14.2

options, 6.3.9

run, 14.1

meshes, 6.3.2, 6.10.5

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

mmff, 9.21.6, 10.4.16, 22.2.17, 22.8.5

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

model, 4.3, 9, 9.1, 9.1.1, 9.1.1.1, 9.1.2, 9.1.2.1, 9.1.2.2, 9.1.3.1, 9.3, 9.8, 9.18, 21.5

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

molecule, 22.2.8, 22.8.3

amino acid, 9.12

editor, 10.4

group, 9.11

moledit, 10.4.8

mol, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13, 21.11.2

molmechanics, 22.9.8

mol2, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6

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

molscreen, 13, 15

administration, 10.10.5

custom model panel, 15.4

run, 15.1

residue, 22.4.13

model type, 15.3

N C, 22.4.14

results, 15.2

mutation, 9.11, 9.13, 9.14, 9.16, 21.5.3, 21.5.4, 22.4.13, 22.4.14

molskin, 6.3.2

protein binding, 9.13

molsynth, 10.11.5

ligand, 9.16

molt, 18, 18.4

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

mouse, 4.4, 6.11, 6.12

nearest, 22.4.22

mov, 6.16, 6.16.2

neural network, 12.4.3.1, 16.18

move, 3.6.3.19, 4.12, 4.14, 5.2.4.2, 6.3.9.1, 6.3.9.2, 6.12, 6.12.7, 9.18, 22.4.5

Torsion Profile Neural Network Prediction Engine, 6.12.6.1

column, 17.1.28

new, 8.1

mesh, 6.3.9.2

icm session, 3.6.1.2

slide, 7.4.2

table, 17.1.1

structure, 6.12

table, 17.1.1

tools, 6

nmr, 22.4.18

rotate, 6.11

model, 4.2.5

slab, 6.11

nnc, 15.3.5

translate, 6.11

nntorsion, 6.12.6.1

z-rotation, 6.11

nof, 10.11.2

zoom, 6.11

chemical, 10.11.2

movie, 6.16.1, 22.2.19, 22.9.7

non-contiguous selection, 4.6.18

montecarlo, 22.9.7

normal modes, 9.21.14

making, 6.16, 6.16.2

nucleic acid conformation analysis, 5.5.12

open, 6.16, 6.16.2

geometry, 5.5.12

mpa, 21.6.11

nucleotide analysis, 5.5.12

mpeg, 6.16, 6.16.1, 6.16.2

conformation, 5.5.12

mpg, 6.16, 6.16.2

geometry, 5.5.12

mpo, 10.34

puckering, 5.5.12

binary classification, 10.34.2

number of sp3, 10.11.2

custom step function, 10.34.1.2

numbers, 10.3.28

customized, 10.34.1

nvidia, 22.1.2

save, 10.34.1.3

obj, 6.7

special cases, 10.34.1.1

object, 4.12, 4.19, 21.3, 22.2.8

mtl, 6.7

objects, 5.1.2

multi apf super, 10.37.7

in table, 17.3

panel, 6.2

in.table, 17.3

parameter optimization, 10.34

occlusion, 6.3.12, 6.10.5

template, 9.1.4.3

shading, 6.3.12

windows, 6.2

effect, 6.10.5

multiple, 12.6.2, 21.12.1

occupancy, 6.1.3, 21.3.10

chain, 9.1.2.2, 9.1.3.1

oda, 5.6.5, 12.13, 12.13.2, 12.13.3

position group scan, 16.7

older version, 3.6.1.10

rec, 12.6.2

omega, 6.8.5, 22.2.18

receptor, 4.16.1, 21.12

online databases, 10.5.5

docking, 16.15

open, 3.6.1.3, 4.18, 17.1.2

protein, 22.2.5

file, 4.18

mutant, 9.11, 22.4.13, 22.4.14

password, 4.18.1

mutate, 9.13, 9.14, 22.4.15

with password, 3.6.1.4

password, 3.6.1.4, 4.18.1

clone, 10.5.6.2

optimal, 5.6.5, 12.13, 12.13.2, 12.13.3

draw2D, 10.5.6.1

optimize, 9.21.2

draw3D, 10.5.6.2

oracle, 19

edit, 10.5.6.1, 10.5.6.2

orange, 4.6.5

move, 10.5.6.2

selection, 4.6.5

new, 10.5.6.2

origin, 6.8.12, 22.2.10

search, 10.5.6, 10.5.6.3, 21.6.5, 21.6.6

orthosteric, 5.6.6

phase angle P, 5.5.12

other selection, 4.6.19

phi, 6.8.5, 22.2.18

outside, 22.5.9

phylogenetic, 8.7.8

overlay, 21.3.3, 22.2.5, 22.4.6

phylogeny, 8.7.8

pH, 10.19

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

pairwise, 10.37.5, 10.37.6

picking, 6

apf score, 10.38

picture, 3.6.1.14, 4.15, 6.15.2, 7.6.3

parallelization, 13.1.7

tips, 4.15

password, 10.10.5

chart, 17.4.8

paste, 10.4.11, 10.4.18, 17.1.35

pipi, 5.2.5

pca, 17.5

pka, 10.15

pdb, 3.6.1.7, 4.2.2, 4.16, 4.16.6, 4.19, 5.1.3, 10.7.1, 21.3, 22.2.24, 22.2.25, 22.4.4

planar, 5.5.7, 6.8.5, 22.2.18

chem gl, 10.7.3

angle, 5.5

iw, 10.7.2

angle, 6.9.2

dormat, 4.19

plane, 6.3.10, 6.13, 6.13.1, 6.14, 22.2.11, 22.2.19, 22.2.21

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

search, 4.2.3, 4.2.4, 21.3.1

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

function, 3.6.9, 3.6.9.1

search, 3.7.4, 4.2, 4.2.1

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

peptide, 4.17, 9.15, 9.20, 12.12

mean median iqr, 17.4.23

docking, 12.12

point label, 17.4.19

modeling, 9.20

preferences, 4.20.8

editor, 16.20

groups, 17.4.25

percentage similarity, 8.7.15, 21.4.4

regression, 17.4.16

perspective, 3.6.3.9, 6.10.6

selection, 17.4.18

ph4, 10.5.6

zoom translate, 17.4.17

draw 2d, 10.5.6.1

axis, 17.4.15

3d, 10.5.6.2

display, 17.4.15

search, 10.5.6.3

grid, 17.4.15

pharmacophore, 10.3.35, 10.5.6.5, 21.8.2

inline, 17.4.22

2D, 21.6.6

logarithmic, 17.4.12

3D, 21.6.5

pls, 10.21, 10.22, 11, 17.6, 21.13

png, 3.6.1.14, 6.15, 6.15.2, 7.6.3, 10.2, 10.2.6

with selection, 22.1.12

pocket, 4.9, 5.2, 5.2.2, 5.2.3, 5.6.6, 21.3.7, 22.2.14, 22.4.11, 22.5.10

prodrug, 10.26

conservation, 22.4.12

profile, 4.16.9, 8.3.8

properties, 5.8

project, 3.6.1.5, 12.13.4, 19.6, 21.6.4.6

surface, 5.2.2, 13.1.11

close, 3.6.1.13

peptide, 4.9

rename, 3.6.1.9

properties, 4.9

properties, 6.8.2, 10.11, 10.11.1, 22.8.7

pocketome, 4.16, 4.16.1, 5.8

property, 10.4.9, 22.8.7, 22.8.8, 22.8.9, 22.8.10

pockets, 5.6.6

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

protein, 5.4.6, 8, 9.15, 22.4.5

postscript, 4.20.6

chain, 9.4

potential mean force, 13.1.4

health, 5.6.3

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

ppt, 7.12, 7.14, 22.3.3

distance, 5.5.6

predict, 8.3.2, 10.21, 10.22, 11, 11.2, 17.6, 22.8.9, 22.8.12

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

preferences, 4.20, 13.1.5, 22.2.24, 22.2.25

surface area, 5.5.5

preferred residues, 9.6

similarity, 5.7

presentation, 7.6.5, 7.7, 7.12

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

components, 11.5

superposition, 5.4

print, 6.7, 17.4.20, 17.7.3

select, 5.4.1

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, 4.20.6

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

probe, 12.2.1.1, 22.5.13

docking refinement, 12.13.11

problem, 22.1.14

protein-proteindocking, 12.13.7

protonated, 22.4.15

racemic, 10.3.28, 10.20.5, 22.5.21

protonation, 10.19, 12.1.4

radar, 17.4.6

state, 12.1.4

rainbow, 4.20.5, 6.8.16, 10.3.35, 22.2.38

protonation_ph, 10.19

ramachandran plot, 5.5, 5.5.10

protonation_ph_charge, 10.19.2

random forest, 11, 21.13

protonation_ph_concentration, 10.19.1

range, 6.10.7.2

protprot, 12.13

rapid isostere replacement, 13.4

proximity, 6.3.3, 6.3.4

ratio.selection, 4.20.5

psa, 10.4.9, 10.11.7

dock ligand, 16.9

pseudorotation P, 5.5.12

reactions, 10.8, 10.35.5

analysis, 5.5.12

reactive cysteine, 5.6.2

phase angle, 5.5.12

reactivity, 10.11.3

psi, 6.8.5, 22.2.18

read, 3.6.1.3, 3.6.1.17, 4.18, 8.1, 10.3.1

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

purple box, 3.6.3.23, 12.2.1.1, 16.9.1

table, 17.1.2

pyramid, 12.1.6

pdb, 4.2, 4.2.1

pyramidal, 12.1.6

table, 17

qs hydrogen bond, 5.2.4

reagent, 10.35.5

pdb chem gl, 5.1.3.2

rear, 6.3.10, 6.13.1

iw, 5.1.3.1

recent files, 3.6.1.17

qsar, 10.21, 10.22, 11.1, 21.13

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

quality, 3.6.1.15, 4.20.5

surface, 16.3.1, 16.3.2

query, 9.1.2, 19, 19.3, 22.8.1, 22.9.5, 22.9.6

flexibility, 21.12.2

molt, 18.4

recover, 3.6.2.11

processing, 10.5.3

cylinders, 8.7.16, 22.6.2

setup, 10.5.1

lines, 8.2, 22.6.1

quick, 4.15

redo, 3.6.2.10, 10.4.11, 16.5.5

image, 6.15.2

refine, 9.8, 9.9

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

regression, 10.36.2, 11.1, 11.5, 17.4.16, 21.13

display.distance, 6.9.1

regul, 9.8

start color, 4.8

regularization, 9.8, 9.21.3

quit, 3.6.1.19

relationship, 11, 17.6

group, 10.28.7, 10.35.4

covalent geometry, 12.2.1.3

table, 10.35.2

relaxed ligand, 16.3.9

groups, 10.35.2

reload, 12.4.5, 22.5.4

r-group, 10.28.7, 10.35.2

dock results, 12.4.5

decomposition, 10.28.7

remove, 22.2.6, 22.2.7, 22.2.10

enumeration, 10.28.7

salt, 22.8.14

r-groups, 17.4.25

explixit.hydrogens, 10.12

rename, 17.1.25

server setup, 13.4.1.1

column, 17.1.25

setup, 13.4.1

project, 3.6.1.9

ridge, 13.5

renumber, 9.2, 22.4.4

right, 4.13

reorder column, 17.1.29

click, 4.13

replace chemical, 10.3.32

rigid, 10.37

replacement, 16.6

substructure superposition to template, 10.37.2

group, 16.8

ring, 5.2.5, 10.4.3, 10.4.6, 10.5.1

report, 19.3

stacking, 5.2.5

representation, 3.6.3.19

rings, 10.3.28, 10.23, 10.37

residue, 4.20.7, 22.2.8, 22.4.15, 22.4.22

rmsd, 5.5, 5.5.2, 22.4.7, 22.4.8

alternative orientation, 21.3.11

rock, 3.6.3.15, 6.10.7, 6.10.7.1, 7

content, 8.3.1

speed, 6.10.7.2

number selection, 22.2.36

root, 22.4.7

range, 4.6.18

mean square deviation, 5.5.2

content, 3.6.4, 8.3, 8.3.1

rotate, 3.6.3.15, 4.4, 6, 6.10.7, 6.10.7.1, 6.12, 6.12.1, 6.12.2, 7, 10.3.34, 22.8.13

mutate, 22.4.13, 22.4.14

chemical, 10.3.34

residues, 5.2.2, 5.2.3, 22.2.14

torsion, 6.12.6.1

resize, 6.3.9.1, 6.15.3

when pasting, 10.4.8

mesh, 6.3.9.1

easy, 3.6.3.12

resolution, 4.2.4

speed, 6.10.7.2

restore, 3.6.2.11, 6.3.10, 6.13.1

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

restraint, 16.12.1, 16.12.2

row, 17, 17.1.22, 17.1.35, 17.1.45

restraints, 14.2

flag, 17.1.13

results, 12.13.10

height, 17.1.7, 22.2.39

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

ribbon, 3.7.1, 4.20.9, 6.1.3, 22.2.23, 22.2.34

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

breaks, 6.1.3

salts, 10.3.18

cylinders, 6.1.3

sample, 9.19, 10.37

smooth, 6.1.3

double bond cis trans, 12.2.1.3

worm, 6.1.3

peptide, 9.20, 9.21.12

ribbonColorStyle, 4.20.9

protein, 9.19, 9.21.11

ribose pseudorotation, 5.5.12

racemic centers, 12.2.1.3

pucker, 5.5.12

sar, 10.28.7, 10.36, 17.4.25

ring, 5.5.12

analysis, 10.36

conformation, 5.5.12

table, 10.36.3

torsion angles, 5.5.12

save, 4.19, 6.3.11, 6.10.7.4, 8.1.5, 10.2.3, 17.4.21, 17.7.3, 22.2.33

ride, 13.4

SMILES, 10.4.15

gpu benchmark, 13.4.1.2

alignment, 8.7.3

pdb, 4.19

script, 4.17, 7.6.4, 7.6.5, 22.4.19, 22.10, 22.10.1, 22.10.2, 22.10.3

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

search, 5.7, 10.10, 10.10.4, 18.2, 19.3, 22.9.6

docked ligand, 16.19

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, 16.19

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

image, 3.6.1.15, 4.15

secondary aliphatic amines, 10.15

object, 4.10

structure, 5.6.1, 22.2.20

password, 3.6.1.11

structure, 3.6.4, 6.1.3, 8.3, 8.3.2

picture, 3.6.1.15

select, 4.6.12, 4.6.13, 17, 17.1.45, 22.4.22

project, 3.6.1.8, 3.6.1.9, 3.6.1.10, 4.11

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

scale, 4.20.5, 22.2.38

graphic, 4.6.16

scan, 9.21.7, 12.4.1

object, 4.6.11

hits, 12.4.1

residue, 4.6.13, 4.6.18

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

new project, 19.6

purple.box, 3.6.3.23

pages, 19.7

residue, 4.6.3

query, 19.3

workspace, 4.6.3

upload data, 19.2

selectall, 3.6.2.3

scare, 12.6.4

selecting.neighbors, 4.6.16

scatter, 13.1.9.2

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

score, 12.4.3.1, 13.1.8, 16.4, 21.8.3, 21.8.5, 22.5.7, 22.5.8, 22.5.18

clear, 3.6.2.7

threshold, 13.1.4

neighbors, 3.6.2.8

screen, 10.38, 21.8.4, 21.9, 21.11.1

alignment, 4.6.19

screening, 13.1, 13.1.1, 13.1.2, 13.5, 14.4, 21.12

all, 3.6.2.3

screenshot, 6.16, 6.16.2

alter, 4.6.7

movie, 6.16.2

atom, 3.6.2.5

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

filter, 3.6.2.5, 4.6.8

set, 10.3.31, 22.4.21

graphical, 4.6.16

formal charges, 10.15

invert, 3.6.2.6, 17.1.23

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

neighbors, 3.6.2.5, 3.6.2.8, 4.6.15, 4.6.17

disulfide, 9.10, 22.4.17

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

shade, 8.7.7, 8.7.7.1

superposition, 5.4.1

alignment, 21.4.4

table, 4.6.19, 17.1.23

shading, 6.3.12

elements, 17.1.23

shadow, 6.10.2

tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8

share model, 11.1.5

whole, 4.6.11

sheet, 22.2.20

workspace, 4.6.9, 4.6.17

shell preferences, 4.20.10

selectioninvert, 3.6.2.6

shift, 6.8.3

selections, 4.6

shine, 3.7.2, 4.20.5

links, 8.3.9

shineStyle, 4.20.3

selectneighbors workspace, 4.6.17

show, 7.3.1, 17.1.39

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

secondary structure, 8.2, 22.6.1

side-by-side, 22.1.19

similarity, 8.7.15

side-chain sampling, 12.13.11

sites, 8.5

side-chains, 12.6.1

structure, 8.3.6

sigmaLevel, 5.3.6, 5.3.7

type, 8.3.4

similarity, 10.31

DNA, 8.3.4

simulation, 14, 14.1, 14.2, 14.3, 14.4, 22.9.8

alignment, 8.3.5, 8.6.2, 8.6.6

length, 22.5.12

amino acid, 8.3.4

simulations, 22.7

nucleotide, 8.3.4

single, 10.4.10

protein, 8.3.4

chain, 9.1.2.1

search, 8.4

singlet, 10.4.7

structure.alignment, 8.3.6, 8.6.3

sites, 5.4.6

sequences, 8, 22.2.25

size, 5.2.4.1

unique, 8.3.13

sketch accents, 6.10.3

extract, 8.3.13

markush, 10.35.1

smiles, 10.4.12

hardware, 3.6.3.7

accents, 3.6.3.14, 6.10.3

side-by-side, 3.6.3.6

skin, 3.7.1, 6.1.4, 22.2.16

stereohard faq, 22.1.6

slab, 6.3.10, 6.13.1

stereoisomer, 10.20.5

slice, 6.13

stereoisomers, 10.25

slide, 6.10.7.4, 7.2, 7.3.1, 7.6.1, 22.2.31

stick, 4.20.5

effects, 7.5

stl, 6.7

movie, 6.16.1

stop, 6.10.7.3

file, 7.2

store, 3.6.3.19, 6.10.7.4, 22.2.22

navigation, 7.3.2

current view, 3.6.3.19

show, 7.3

faq, 22.2.22

blend, 7.5

strain, 5.6.3, 6.12.6.1, 10.17, 10.27, 10.27.2, 12.1.10, 12.4.3.1, 16.4

edit, 7.4.1

strip, 22.4.9

effect, 7.5

structure, 5.3.3, 11, 17.6, 21.3, 22.4

smooth, 7.5

analysis, 5.5.12, 21.3.4

transition, 7.5

ensemble, 9.21.14

slides, 6.16.1, 7, 7.1, 7.3, 22.2.30

representation, 6.1

smiles, 10.4.9, 10.11, 10.20, 10.20.3, 10.20.4

smiles, 10.20.4

smooth, 6.3.9.3

structure-based, 13

surface, 22.2.37

structures, 10, 10.1

solid, 6.3.9.3

style, 4.20.5

solvent.accessible.area, 22.4.19

substituent, 10.9.1, 10.9.2, 10.35.2, 16.5.2

sort hitlist, 13.1.9.1

substructure, 10.10.4, 10.13, 10.37.1, 10.37.2, 12.7, 22.8.1, 22.9.5

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

superimpose, 3.6.8, 5.4.2, 5.4.6, 10.37.4, 21.3.3, 22.2.5, 22.4.6, 22.4.7, 22.4.8

speed, 6.10.7.2

3D, 5.4.3

sphere, 22.4.11

Calpha, 5.4.3

spherical, 22.4.9, 22.4.12

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

stability, 9.14, 21.5.3, 21.5.4

superposition, 10.37, 10.37.1, 10.37.2, 10.37.5, 10.37.6, 21.3.3, 21.8.1

stack, 9.19, 9.21.18, 12.4, 12.13.10, 22.9.8

surface, 3.7.1, 4.20.5, 5.2.2, 5.2.3, 6.1.6, 6.3, 6.3.3, 6.3.4, 22.2.16, 22.2.37, 22.4.19

calculations, 9.21.18

area, 5.5

stacking, 5.2.5

area, 5.5.5

standalone hitlist, 12.4.4

surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5

standard table, 17.1

surrounding, 22.4.11

standardize, 10.12

swissprot, 8.1, 8.5

table, 10.12

sxstrace, 22.1.19

start, 10.10.2

symmetric oligomer, 9.1.3

startup, 22.10.2

symmetry, 5.3.1, 5.3.3, 21.3.8, 21.3.9

static, 22.4.8

synthesize, 10.11.5

stereo, 4.20.6, 6.6, 10.3.28, 10.4.2, 22.1, 22.1.6, 22.1.7, 22.1.14

synthetic feasibility, 10.11.5

bond, 10.4.2

system preferences, 4.20.11

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

excel, 10.3.10, 17.1.20

color, 17.1.10

filter, 10.3.12, 17.1.43

column format, 17.1.40

find-replace, 10.3.13

copy, 17.1.36, 17.1.37

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

merge, 3.6.10.5, 10.3.23, 10.32

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, 10.3.11, 17.1.4, 17.1.19

print, 17.1.19

read, 17.1.2

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

save, 10.3.9, 17.1.3, 17.1.4, 17.1.21

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

sort, 3.6.10.4, 10.3.5, 17.1.42

save, 17.1.8

standard, 17.1

zoom translate, 10.3.30

view, 10.3.29

action, 17.1.47

width, 17.1.4

alignment, 17.1.12

tables, 10.31, 17

append, 17.1.43

tag, 4.6.21, 16.5.7, 17.1.46

clone, 17.1.16

tags, 4.6.21

color, 17.1.10

m, 5.5.12

column, 10.3.4, 17.1.26, 17.1.32, 17.1.39

tautomer, 10.24, 22.4.15

columns, 10.3.8

tautomers, 10.24

compare, 10.3.22

temperature, 5.6.4

copy, 10.3.6

template, 9.1.2, 10.4.6, 10.37

cursor, 17.1.47

docking, 22.5.3

delete, 17.1.14, 17.1.17

templates, 10.4.6

font size, 22.2.1

crash qlock, 22.1.13

tether, 12.5, 16.12.1, 16.12.2

tsv, 17.1.21

text, 4.20.7, 7.6, 7.6.1, 7.6.7, 10.3.28, 10.10.4, 17.4.24, 22.9.6

tut analyze alternative orientations, 21.3.11

search, 10.5.4

occupancy, 21.3.10

texture, 3.7.6

symmetry, 21.3.9

thoroughness, 10.23, 10.37, 22.5.12

multiple receptor, 21.12.1

three, 10.3.24, 22.8.6

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

two, 10.3.24, 22.8.6

predict, 3.6.10.2

ubuntu, 22.1.18

tooltip, 17.4.26

ultra large library, 13.5

balloons, 17.4.26

unclip, 6.3.10, 6.13.1

torsion, 6.12.6, 6.12.6.1, 9.21.7, 10.17, 16.5.4, 22.4.16

undisplay, 4.5, 6.1.7, 22.2.10, 22.2.32

analysis, 10.16

box shade font, 8.7.7.1

angles, 6.12, 6.12.6

undisplay-all, 3.6.3.1

free strain, 10.17

origin, 6.8.12

scan, 9.21.7

undo, 3.6.2.9, 4.20, 10.4.11, 16.5.5

toxscore, 10.11.3

redo, 16.5.5

trace, 6.1.10

uniprot, 4.16.5, 8.5

transition.blend, 22.2.31

unique, 10.3.28, 10.33

transitions, 7, 22.2.30

unit, 5.3.3

translate, 4.4, 6, 6.12, 10.3.30

units, 22.5.1

translation, 6.12.3, 8.3.3, 17.4.17

unix, 22.10.2

transparent, 6.3.9.3

unsatisfied hydrogen bonds, 16.3.8

background, 6.15.3

unusual peptide, 4.17

ribbon, 22.2.3

upload, 19.2

surface, 22.2.37

use activeicm, 7.12

tree, 8.7.8, 10.28.7, 17.7.2, 17.7.3, 17.7.4

user, 10.10.5, 19.5

branch swapping, 8.7.8

defined groups, 16.5.3

distance, 10.28.3

modifiers, 16.5.3

edit, 10.28.4

user-defined groups, 10.4.5

reorder, 10.28.3

van der waal, 6.8.15

triplet, 10.4.7

variable, 4.20.7, 22.2.8

trouble shooting, 22.1.11

verbose, 10.23

trouble-shooting, 22.1.12

large sdf files, 10.1.2

truncating a mesh object, 22.2.15

vicinity, 10.23

view, 3.6.3.19, 7.3.1, 10.3.28, 22.2.22, 22.9.8

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

windows, 4.14.1, 10.10.1

dock results, 12.4

wire, 3.7.1, 4.20.5, 6.1.1, 22.2.4, 22.2.21

fog, 3.6.3.5

wireBondSeparation, 4.20.1

macroshape, 3.6.3.22

working directory, 22.5.23

menu, 3.6.3

workspace, 4.5, 5.1.3.1, 10.7.2

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

write, 4.15, 4.19, 17.4.21, 22.9.4, 22.9.7

shadow, 3.6.3.13

alignment, 8.7.3

sketch accents, 3.6.3.14

excel, 10.2.3

slide show, 7.3.1

image, 3.6.1.15, 22.1.20

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

virtual, 13.1, 13.1.1, 13.1.2, 21.9, 21.11.1

picture, 3.6.1.15

ligand screening, 15

project, 3.6.1.8, 4.11

screen, 13.3, 13.4

table, 17.1.3

screening, 13, 13.2

writing a pdb file, 22.4.3

examples, 21.11

ray, 3.6.5

virus, 5.3.3

xi, 6.8.5, 22.2.18

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

xstick, 6.1.2, 22.2.21

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

zoom, 4.4, 6, 6.12, 6.12.4, 10.3.30, 17.4.17

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

run, 13.1.6

score, 12.1.9

visualization, 13.1.11

results, 13.1.8

volume, 10.4.9

water, 9.21.17, 12.1.8

waters, 9.21.17

wavefront, 3.7.6, 6.3.11, 6.7

weak, 22.4.20

web, 21.2

browser, 3.6.1.12

weight, 10.11, 22.8.7, 22.8.10