ICM User's Guide: Index

modify group, 9.12.2

Altona-Sundaralingam pseudorotation, 5.5.12

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

Area, 9.22.18, 22.2.26

Chemical Label, 6.8.11

Atom Single Style, 4.20.3

Interaction Diagram, 16.3.7

Atomic Property Fields, 11.4, 21.14

bioisostere, 10.9.1

Bad Groups, 22.8.7, 22.8.10

chemical label, 6.8.11

Baell, 10.4.9

from PDB, 10.1.1

Beep, 4.20.11

interaction diagram, 10.6

Beta-Catenin, 16.21

screening, 15

Bioactive Conformation, 16.21

to 3D, 10.20, 10.20.3

Blast, 22.2.25

depiction, 10.20.2

BlastDB Directory, 4.20.2

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

alphas, 6.8.3

QSAR, 10.38.4, 11.4, 21.14

C-alpha backbone, 5.5.11

chemical, 10.4.16, 10.20.1

C2′-endo pucker, 5.5.12

interactive ligand editor, 3.7.5

C3′-endo pucker, 5.5.12

ligand editor, 16.3.4

CHEMRIYA, 13.5

object, 6.3.9

COLLADA, 3.6.1.7

pharmacophore, 13.3, 16.3.11

CPK, 3.7.1

print, 6.7

CYM, 9.12, 9.12.1

printing, 6.7

CYS, 9.12, 9.12.1

screening, 15

ChEMBL, 4.16.2, 10.1

stereo, 6.6

Chemical Cluster, 21.6.3

visualization, 5.5.11

Search, 21.6.2

3DMOLT, 18.5

CisTransAmide Angle, 13.1.9.4

3DQsar, 11.4

Clash Threshold, 4.20.10

3D_Similarity_PDB_Search, 5.7

Computational Chemistry, 16.21

3Dqsar tutorial, 21.14

Computer-Aided Drug Discovery (CADD), 16.21

bioisostere, 10.9.2

Covalent Geometry., 16.21

predict, 5.6

DILI, 10.11.5

helices strands, 5.6.1

DNA, 4.17, 8, 8.3.3

local flexibility, 5.6.5

Decomposition, 10.36.3

protein health, 5.6.4

Design Evolution, 12.10

tools identify ligand binding pocket, 5.6.7

Dimer, 5.5.11

oda, 5.6.6

Display, 22.2.26

4D, 12.6.2, 21.12.1

Distance, 13.1.9.4

dock, 16.15

Dock Directory, 4.20.2

docking, 4.16.1

Docking, 22.2.26

64, 22.1.3

Drug Bank, 4.16.7

A-form RNA, 5.5.12

Design, 16.21

AI, 12.10

Editor, 4.20.2

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

Eintl, 12.1.10

template, 10.37.3

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

ARG, 9.12, 9.12.1

Extended Amino Acids, 16.21

ARN, 9.12, 9.12.1

FILTER.Z, 4.20.2

ASP, 9.12, 9.12.1

gz, 4.20.2

ASPH, 9.12, 9.12.1

uue, 4.20.2

Acetyl Cap, 16.21

FTP.createFile, 4.20.11

ActiveICM, 3.6.1.12

keep File, 4.20.11

Alignment mode, 5.5.11

proxy, 4.20.11

Alpha-Helix Stabilization, 16.21

Filter.zip, 4.20.2

Force Auto Bond Typing, 4.20.11

resLabelDrag, 4.20.7

Formula, 22.8.7, 22.8.10

resize Keep Scale, 4.20.3

Free Wilson, 10.36.2

ribbonRatio, 4.20.9

Frequently Asked Questions, 22

ribbonWidth, 4.20.9

GAMESS, 9.22.16

ribbonWorm, 4.20.9

GIF, 3.6.1.15, 6.16, 6.16.2

rocking, 4.20.4

GINGER, 10.23

Range, 4.20.4

GLU, 9.12, 9.12.1

Speed, 4.20.4

GLUH, 9.12, 9.12.1

selectionStyle, 4.20.3

GPCR Modeling Example, 21.5.1

site Label Drag, 4.20.7

GRAPHIC.store Display, 4.20.3

Shift, 4.20.7

NtoC Rainbow, 4.20.4

siteArrow, 4.20.7

alignment Rainbow, 4.20.4

stereoMode, 4.20.3

atomLabelShift, 4.20.7

stickRadius, 4.20.1

ballStickRatio, 4.20.1

surfaceDotDensity, 4.20.3

center Follows Clipping, 4.20.3

surfaceDotSize, 4.20.3

clash Style, 4.20.3

surfaceProbeRadius, 4.20.3

clashWidth, 4.20.3

transparency, 4.20.3

clip Grobs, 4.20.3

wire Width, 4.20.1

Skin, 4.20.3

wormRadius, 4.20.9

Static, 4.20.3

xstick Backbone Ratio, 4.20.1

discrete Rainbow, 4.20.4

Hydrogen Ratio, 4.20.1

displayLineLabels, 4.20.7

Style, 4.20.1

displayMapBox, 4.20.3

Vw Ratio, 4.20.1

distance Label Drag, 4.20.1

GROB.arrowRadius, 4.20.3

dnaBallRadius, 4.20.9

atomSphereRadius, 4.20.3

dnaRibbonRatio, 4.20.9

contourSigmaIncrement, 4.20.3

dnaRibbonWidth, 4.20.9

relArrow Size, 4.20.3

dnaRibbonWorm, 4.20.9

relArrowHead, 4.20.3

dnaStickRadius, 4.20.9

GUI.auto Save, 4.20.4

dnaWormRadius, 4.20.9

Interval, 4.20.4

font Scale, 4.20.7

autoSave, 22.2.33

fontColor, 4.20.7

autoSaveInterval, 22.2.33

fontLineSpacing, 4.20.7

enumeration Memory Limit, 4.20.11

grobLineWidth, 4.20.3

max Nof Recent Files, 4.20.11

hbond Ball Period, 4.20.1

Sequence Length, 4.20.4

Style, 4.20.1

splash Screen Delay, 4.20.11

hbondAngleSharpness, 4.20.1

Image, 4.20.11

hbondMinStrength, 4.20.1

table Row Mark Colors, 4.20.4

hbondStyle, 4.20.1

workspace Folder Style, 4.20.4

hbondWidth, 4.20.1

workspaceTabStyle, 4.20.4

hetatmZoom, 4.20.1

GigaScreen, 18.5

hydrogenDisplay, 4.20.1

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

HID, 9.12, 9.12.1

mapLineWidth, 4.20.3

HIE, 9.12, 9.12.1

occupancy Radius Ratio, 4.20.3

HIP, 9.12, 9.12.1

occupancyDisplay, 4.20.3

HIS, 9.12, 9.12.1

quality, 4.20.3

HTTP.proxy, 4.20.11

rainbow Bar Style, 4.20.4

support Cookies, 4.20.11

Hbond to selection, 13.1.9.4

LYN, 9.12, 9.12.1

Hbonds, 16.3.4

LYS, 9.12, 9.12.1

Helicon Peptide, 16.21

LigStrain, 16.21

Homodimer, 5.5.11

Ligand Strain, 16.21

Homologous chains, 5.5.11

Liver Toxicity Models, 10.11.5

To Guide, 3

Log Directory, 4.20.2

Html, 4.2.7

LogP, 11, 17.6

Http Read Style, 4.20.11

LogS, 11, 17.6

Hydrocarbon Staples, 16.21

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

Hydrogen.bond, 4.20.5

Q and A, 14.5

I+4 Staple Position, 16.21

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

Staple Position, 16.21

MOL2, 13.1.3

ICM Browser How To, 3.1

MOLT, 18.1

Pro How To, 3.2

MOVIE.frame Grab Mode, 4.20.4

analysis tools, 5.5.12

MPO, 10.34

graphics crash, 22.1.11

Mac, 22.1.15

object, 5.6.2, 9.19

Atom Margin, 4.20.10

start, 1

Sigma Level, 4.20.10

ICM-Pro Tutorial, 16.21

Markush, 21.6.9

IMAGE.bondLength2D, 4.20.6

create, 21.6.7

color, 4.20.6

File Size Mb, 4.20.11

compress, 4.20.6

Max_Fused_Rings, 10.11

gammaCorrection, 4.20.6

Mnconf, 4.20.10

generateAlpha, 4.20.6

Model, 11.4

lineWidth, 4.20.6

Modify Amino Acid, 9.12

lineWidth2D, 4.20.6

MolCart, 22.9

orientation, 4.20.6

MolIPSA, 22.8.7, 22.8.10

paper Size, 4.20.6

MolLogP, 22.8.7, 22.8.10

previewResolution, 4.20.6

MolLogS, 22.8.7, 22.8.10

previewer, 4.20.6

MolPSA, 10.11

print, 4.20.6

MolScreen, 15

printerDPI, 4.20.6

MolSoft ICM-Pro, 16.21

scale, 4.20.6

MolVol, 10.11

stereoAngle, 4.20.6

Molcart, 10.5.3

stereoBase, 4.20.6

MoldHf, 10.11, 22.8.7, 22.8.10

stereoText, 4.20.6

Molecular Docking, 16.21

INCHI, 10.20.3

Dynamics, 14.5

IQR, 17.4.6

Preparation, 16.21

ISIS, 22.8.3

Movie.fade Nof Frames, 4.20.4

Icm Prompt, 4.20.10

quality, 4.20.4

InChi, 10.3.20, 10.4.12, 10.20.3

Auto, 4.20.4

key, 10.3.20

Multimer, 5.5.11

Interaction Diagram 2D, 16.3.7

NCBI, 22.2.25

Interactive Ligand Editor, 16.21

NH2 Cap, 16.21

Plot, 5.5.12

NVIDIA, 22.1

Internal Coordinates Table, 9.22.13

Natural Amino Acids, 16.21

Directory, 4.20.2

NephroTox, 10.11.4

JPEG, 3.6.1.15

Nof_Atoms, 10.11

KMZ, 3.6.1.7

Nof_Chirals, 10.11

LCC, 13.5

Nof_HBA, 10.11

Nof_Rings, 10.11

Projects Directory, 4.20.2

Nof_RotBonds, 10.11

Prosite Dat, 4.20.2

Non-overlap, 13.1.9.4

Protein, 22.2.26

North conformation, 5.5.12

complex, 5.5.11

Nvidia GL failutre, 22.1.11

Protein-Peptide Interactions, 16.21

ODA, 22.2.26

Viewer, 4.20.2

Optimal, 22.2.26

Pseudorotation Interactive Plot, 5.5.12

Output Directory, 4.20.2

Pub Chem, 4.16.8

PAINS, 10.4.9, 10.11.3

PubMed Reference, 17.1.40

chemicals, 10.4.9

Pubchem, 4.16.8

PCA, 11.1, 11.5, 21.6.4

QSAR, 11, 11.1, 17.6, 21.14

analysis, 10.29

R, 10.8, 10.36.1

PDB, 4.2.7, 5.1.2, 5.3.3, 5.7, 8.1, 10.1.1, 16.20

and S, 22.5.21

7UWI, 16.21

R-Group, 10.36.3

Directory, 4.20.2

R-groups, 16.5.3

Style, 4.20.2

REAL, 10.5.5, 13.5

link, 17.1.40

RIDE, 18.5

Search, 3.6.2.12, 3.6.2.13, 3.6.2.14, 3.6.2.15, 3.6.2.16

RIDGE, 18.5

Field, 3.6.2.13

- Rapid Docking GPU Engine, 13.5

Homology, 3.6.2.15

RMSD, 5.4.2, 9.22.18

Identity, 3.6.2.14

RMSF, 9.22.18

Sequence, 3.6.2.16

RNA, 4.17

convert, 5.1.2

backbone conformation, 5.5.12

PFAM, 3.6.1.7

chain analysis, 5.5.12

PLOT.Yratio, 4.20.8

conformation, 5.5.12

color, 4.20.8

pucker, 5.5.12

date, 4.20.8

structure analysis, 5.5.12

draw Tics, 4.20.8

sugar conformation, 5.5.12

font, 4.20.8

RTCNN, 12.1.9, 12.4.3.1

fontSize, 4.20.8

Score, 16.21

labelFont, 4.20.8

Ramachandran Plot, 5.5.9

lineWidth, 4.20.8

Real Format, 4.20.10

logo, 4.20.8

Reinforce Helix Tool, 16.21

markSize, 4.20.8

Relax Geometry Command, 16.21

orientation, 4.20.8

Label Shift, 4.20.7

paper Size, 4.20.8

Style, 4.20.7

previewer, 4.20.8

Residue Replacement, 16.21

rainbowStyle, 4.20.8

RotB, 22.8.7, 22.8.10

seriesLabels, 4.20.8

Rotation angle, 5.5.11

PLS, 11.1

Rotational symmetry axis, 5.5.11

PNG, 3.6.1.15, 4.15, 6.16, 6.16.2

SALI, 10.36.5, 21.6.11

PROPKA, 5.6.2

SAR, 11, 15.6, 17.4.25, 17.6

PROTAC, 12.14

table, 10.36.3, 21.6.9

PSA, 10.11.9

SCARE, 12.6.4

Peptide Engineering, 16.21

SCORE, 22.5.6, 22.5.17

Mode, 16.21

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

Modeling, 16.21

SEQUENCE.site Colors, 4.20.4

Stapling, 16.21

SITE.label Style, 4.20.7

Pharmacophore RMSD, 13.1.9.4

labelOffset, 4.20.7

PowerPoint, 21.2, 22.3

wrap Comment, 4.20.7

Fog, 4.20.4

advanced, 7.14

SMILES, 10.1.2, 10.2.4, 10.4.12

background images, 7.15

Score, 12.1.9, 12.4.3.1

control, 7.13

Select Min Grad, 4.20.10

activeicmjs, 7.16

Sequence Editing, 16.21

activity, 11, 17.6

Show Res Code In Selection, 4.20.7

cliff, 10.36.5, 10.36.6, 21.6.11

Sidechain Optimization, 16.21

tutorial, 21.6.11

Smiles, 22.8.7, 22.8.10, 22.8.11

add database, 10.10.3

South conformation, 5.5.12

new data, 10.3.7

Special Cases, 10.34.1.1

to table, 16.5.7

Strain, 12.4.3.1

adding fragment, 10.4.8

Structural alignment, 5.5.11

in editor, 10.4.8

Subunits, 5.5.11

adjust row height, 22.2.39

SureChEMBL, 4.16.3

administration, 10.10.5

Swissprot, 3.6.1.7

advanced alignment selection, 8.7.14

Dat, 4.20.2

ai, 16.18

link, 17.1.40

decoration, 16.18

Symmetry, 5.5.11

alanine, 12.6.4

TYM, 9.12, 9.12.1

album, 6.15.3

TYR, 9.12, 9.12.1

alias, 10.4.5

Temp Directory, 4.20.2

align, 4.12, 10.14

Terminal Capping, 16.21

color 2D scaffold, 10.14

Tools Analysis, 5.5.12

dna protein, 8.6.4

Torsion Minimization, 16.21

multiple, 8.6.5

Trimer, 5.5.11

sequence structure, 8.6.3

USER.email, 4.20.11

two sequences, 8.6.2

friends, 4.20.11

DNA to protein, 8.6.4

full Name, 4.20.11

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

cut, 8.3.11

super, 10.37.3

display title, 8.7.10

template, 16.12.3

editor, 8.7

tools, 10.38

extract, 8.3.10

3DQSAR, 10.38.4

gaps, 8.7.11

consensus ph4, 10.38.1

horizontal scroll, 8.7.10

pairwise score, 10.38.2

image, 8.7.2

screen, 10.38.3

multiple, 8.3.7, 8.6.5

tutorial, 21.8

options, 8.7.10

cluster, 21.8.5

rename, 8.7.10

consensus, 21.8.2

reorder, 8.3.12

score, 21.8.3

ruler, 8.7.10

screen, 21.8.4

save, 8.7.2

superposition, 21.8.1

search, 8.7.12

alignment, 10.37.7

selection, 8.7.13, 8.7.14

apf3Dqsa, 22.8.12

sequence offset, 8.7.10

apo, 13.1.10

table, 8.7.10

append, 17.1.44

view, 8.7.10

table, 17.1.44

alignments, 8.6, 21.4

rows, 3.6.10.7

allosteric, 5.6.7

applying prediction models, 11.2

alpha, 3.7.2

area, 5.5.3, 5.6.6, 12.13, 12.13.2, 12.13.3, 21.3.5

channel, 4.20.6

aromatic, 10.3.28, 10.38.1

alphaFold, 4.3

arrange, 4.14.1

alphafold, 4.3

window, 4.14.1

ambient, 3.7.2

graph, 22.2.8

amidinium, 10.15

as2_graph, 4.6.5

amino acid, 4.17, 9.12

as_graph, 22.2.8

acids, 9.12.1, 10.4.6

asparagine, 9.22.2

anaglyph, 6.6, 22.1, 22.1.8

assign, 6.1.3

stereo faq, 22.1.8

2D coordinates, 10.20.2

analysis, 3.6.4, 8.3

helices, 5.6.1

charge states amino acids, 9.12

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

options, 17.4.10

boat, 22.5.20

grid, 17.4.10

boltz, 4.3

range, 17.4.10

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

title, 17.4.10

covalent, 22.4.2

b-factor, 5.6.5, 21.3.10

type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3

coloring scale, 22.2.38

bonding, 6.1.8

backbone, 6.1.10, 22.2.13

preferences, 4.20.1

background, 6.4.2, 6.4.3

box, 4.20.7, 6.8.16, 8.7.7, 8.7.7.1, 22.5.9

color shortcut, 22.2.2

alignment, 21.4.4

images activeicm, 7.15

size, 16.9.1

image, 6.4.3

browse, 10.3.31, 12.4.1, 19.4

backup, 3.6.2.11

mode, 10.3.31

bad, 10.11

molt, 18.2

groups, 10.4.9

stack, 9.22.15

ball, 4.20.5

build, 6.10.7.1

and stick, 3.7.1

2D qsar, 11.1.2

balloon, 17.4.26

homology model, 9.1.2

bases, 10.4.6

hydrogens, 9.22.5

basicsel, 4.6.2

buried molSurface, 13.1.9.4

batch, 12.3.2, 12.13.9

buttons, 7.14

file, 12.3.2.2

bye, 3.6.1.19

index, 12.3.2.4

alpha, 6.1.10

loaded icm object, 12.3.2.1

trace, 6.1.10

mol mol2, 12.3.2.3

ca-trace, 6.1.10

molcart, 12.3.2.5

cache, 7.14.1

run, 12.3.3

calculate, 10.11, 22.5.2

bayesian classifier, 11

properties, 10.11

bbb, 10.11.6

sequence similarity, 8.7.15

beep, 22.2.35

startup, 22.10.2

begin docking simulation, 12.3

carbon, 22.2.4, 22.2.5

best, 10.3.34

carboxylic acid, 10.15

bicyclics, 10.4.6

cartesian, 10.23

binding, 21.5.3, 22.2.14, 22.5.2, 22.5.10

cation, 5.2.5

pocket, 9.19

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, 10.11.6

selection, 4.6.7

blue lines, 8.2

speed range, 6.10.7.2

charge, 3.6.3.21, 5.1.3, 5.1.3.1, 5.1.3.2, 6.8.2, 9.12.1, 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

convert, 5.1.3, 5.1.3.1, 5.1.3.2, 9.22.1, 10.7, 10.7.1, 10.7.2, 10.7.3, 22.4.1

groups, 12.2.1.3, 22.5.22

display.fit, 22.8.13

states, 9.12, 9.12.1

draw, 10.4.1

check box, 7.6.6

duplicates, 10.3.21

convert, 22.8.5

editor, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6

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

image, 10.2.6

query, 10.4.3, 10.5.1, 10.5.3

table, 10.2.2

read, 10.1

super, 10.37

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

view, 10.3.28

search, 10.4.3, 10.5, 10.5.1, 10.5.3

chembl, 4.16.2, 4.16.3

similarity, 10.4.3, 10.5, 10.5.1, 10.5.3

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

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

clustering, 10.28, 10.28.6

structure, 10.4.13

descriptors, 22.8.15

superposition, 10.37.3, 10.37.7

dictionary, 10.4.4, 10.4.5, 10.4.6

table, 10.3, 17.2

draw, 21.6.1

cheminformatics, 10, 10.3, 22.8

spreadsheet tutorial, 21.6.1

tutorials, 21.6

edit buttons, 10.4.11

chemistry, 10.24, 22.8

editor, 10.4, 10.4.8

convert, 10.20

not starting, 22.1.13

2dto3d, 10.20.1

fingerprint, 15

pca, 10.29

fingerprints, 22.8.15

smiles, 10.20.3

fragments, 10.3.33

duplicates, 10.33

group, 10.4.5

remove.redundant, 10.33

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

click, 4.13, 6.11, 6.12

display style, 4.20.9

clip, 6.3.10, 6.13.1, 22.2.11

command, 22.5.16

clipboard, 6.15.3, 17.7.3

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

compare, 10.3.29, 10.31, 10.32

clone, 3.6.1.2

table, 10.3.22

close, 6.3.3, 6.3.4, 16.23

tables, 10.31

downstream cluster, 10.28.5

compatible, 3.6.1.10

project, 16.23

complex, 10.6, 13.1.9.3

cavities, 5.6.7

compound, 4.2.4, 10.24, 17.2

cloud, 13.1.7, 13.1.7.2

compounds, 22.9.3

cluster, 9.22.18, 13.1.7, 13.1.9.5, 17.7.1

compress, 4.20.6

stack, 9.22.18

compressed, 17.1.6

representative.center, 10.28.2

table view, 17.1.6

clustering, 17.7, 21.6.3

conditions, 10.5.2

cns, 10.34

gen, 10.23

collada, 3.7.6, 6.3.7

configuration error, 22.1.19

color, 5.6.4, 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

conformation, 9.22.18, 10.23, 12.6.2

alignment, 8.7.9

conformational entropy, 10.27

background, 6.4.2

conformations, 22.9.8

by, 6.4

conformers, 10.23

alignment, 8.8

connect, 6.3.9.1, 6.12, 6.12.7

chemical, 10.3.35

object, 6.12.7

faq, 22.2.20

connectivity, 10.4.3, 10.5.1

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

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

bond, 5.6.3, 21.9.3

decomposition, 10.35.4, 10.36.1, 17.4.25

docking, 12.8, 12.8.1, 16.16, 21.9.3

decoration, 16.18

tutorial, 21.9.3

default, 4.14

cpk, 6.1.5, 22.2.21

delete, 3.6.2.1, 4.6.6, 7.6.8, 22.4.9

crash, 3.6.2.11

alignment, 8.7.5

creat, 7.6.1

all, 3.6.2.2

create, 17.1.1

column row, 17.1.38

markush, 10.35.3

label, 6.8.9

new objects, 4.17

alignment, 8.7.5

cross, 22.2.10

all, 3.6.2.2

section, 6.13

angle.label, 6.9.4

cryptic, 5.6.7

column, 17.1.38

crystal, 5.3.2

distance.label, 6.9.4

crystallographic analysis, 5.3

label, 6.8.9

biomolecule, 5.3.3

row, 17.1.38

contour map, 5.3.6

selection, 3.6.2.1

convert2grid, 5.3.7

tether, 9.22.5

crystallographic cell, 5.3.2

dendrogram, 10.30.1

load eds, 5.3.4

denovo, 12.9

maps cell, 5.3.5

density, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28

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, 9.22.10

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, 9.21

dihedral, 6.9.3

cys, 5.6.3

distance restraints, 6.8.14

cysteine reactivity, 5.6.3

distance2, 6.9.1

damaged skin, 22.1.12

angles, 6.9

dash, 22.2.12

formal charge, 6.1.9

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

gradient, 6.8.17

hbonds, 13.1.9.4, 16.3.4

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, 5.6.6, 12, 12.1, 12.2, 12.2.1, 12.4.5, 12.6, 12.6.1, 12.6.2, 12.6.3, 12.13, 12.13.1, 12.13.2, 12.13.3, 12.13.4, 12.13.5, 12.13.6, 12.13.8, 12.13.9, 12.13.10, 13.1, 13.1.1, 13.1.2, 13.1.6, 13.2, 13.5, 16.10, 16.10.1, 16.11, 21.9, 21.9.1, 21.9.2, 21.11.3, 21.12, 21.12.2, 22.5, 22.5.1, 22.5.9, 22.5.17, 22.5.18

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

tab, 3.7.1, 22.2.16

explicit group, 21.12.2

tether, 6.8.13

from table, 12.3.1.1, 12.3.1.2

toggle, 6.8.16

macrocycles, 12.2.1.3

CPK, 6.1.5

maps, 12.2.1.1, 12.2.1.2

angle, 6.9.2

preferences, 12.2.1.3

chemical, 10.3.3

database scan, 12.2.1.3.2

dihedral.angle, 6.9.3

display, 12.2.1.3.3

distance, 6.8.10, 6.8.14, 6.9.1

general, 12.2.1.3.1

electrostatic, 3.6.3.21

project, 13.1.5

energy.gradient, 6.8.17

table, 13.1.5

hydrogen, 6.1.7

results display, 12.4.6

polar, 6.1.7

setup, 22.5.13

macroshape, 6.3.6

start, 12.2.1

meshes, 6.3.5

steps, 12.2

and display.macroshape, 3.7.6

template, 12.7

molecule, 10.3.24

templates, 16.12.3

origin, 6.8.12

tutorials, 21.9

potential, 3.6.3.21

waters, 12.1.8

representations, 3.7.1

background, 22.5.19

restraints, 6.8.14

batch, 12.3.2

ribbon, 6.1.3

conformations, 22.5.20

skin, 6.1.4

flexible.rings, 22.5.20

status, 22.2.32

hitlist, 12.4.3

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

dpc, 15.3.4

surface, 6.3

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

electrostatics, 6.3.1, 12.13.8

and drop sequences, 8.6.6

elegant sketch, 6.10.4

residue label, 3.6.3.16

element, 10.4.10

draganddrop, 4.12

eln, 19.7

draw, 10.4.18, 10.35.5, 22.8.2

embed browser, 7.11

chemical, 10.4.1

powerpoint03, 7.8

drop, 4.12, 7.6.4, 8.6.6, 22.4.5

powerpoint07, 7.9

drug, 10.11, 22.8.7, 22.8.9

powerpoint10, 7.10

bank, 4.16, 4.16.7, 10.1

activeicm, 7.13

like, 10.11.6

script, 7.13

drugbank, 10.1

browser, 7.7, 7.11

druglikeness, 10.4.9

firefox, 7.7, 7.11

dsPocket, 4.9

internet.explorer, 7.7, 7.11

dual alanine scanning, 12.6.4

microsoft, 7.7

easy rotate, 3.6.3.12

powerpoint, 7.7, 7.8, 7.9, 7.10

ecfp, 11.3

empty hostid, 22.1.18

edit, 5.2.4.1, 16.5.8, 22.8.3

enamine, 10.5.5

2D, 16.5.1

real, 13.5

add sequence, 10.4.17

enantiomer, 22.5.21

alignment, 8.7.1

enantiomers, 12.1.3

chemical moledit, 10.3.26

endocyclic torsion angles, 5.5.12

ligand, 16.5, 16.5.1

energy, 5.6.4, 6.8.15, 10.27, 10.27.2, 12.4.2, 22.5.1, 22.5.2, 22.9.8

2D, 16.5.1

circles, 13.1.11

editor preferences, 16.2

maps, 12.2.1.1, 12.2.1.2

multiple substituents, 16.5.2

terms, 9.22.19

tools, 3.6.2.17

ensemble, 12.6.2

menu, 3.6.2

calculations, 9.22.18

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

point, 16.19

electron, 5.3.4, 5.3.6, 5.3.7, 22.2.27, 22.2.28

explicit, 10.3.28, 12.6.1

denisty map, 5.3.5

flex, 12.6.1

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

group, 12.6.3

contour, 3.6.5

docking, 12.6.3

electrostatic coloring scale, 22.2.38

groups, 21.12.2

potential, 3.6.3.21

export, 5.5.10, 19.4

pdb, 4.19

dollar, 22.10.3

extra windows, 6.2

download install, 22.1.1

extract, 4.18.2, 8.1, 10.1.3, 22.4.12, 22.8.8

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, 4.18.2

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

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

gl failure, 22.1.11

ISISdraw, 22.8.3

gui, 22.2

MolCart, 22.9

guided dock, 22.5.3

activeicm, 22.3

hitlist, 22.5.7

path, 22.3.3

hydrogen bond acceptors, 22.8.17

alignment secondary structure, 22.6.2

iSee, 22.2.30

apf model, 22.8.12

icmPocketFinder, 22.5.10

atom charge, 22.4.21

insert column, 22.8.7

display, 22.2.17

installation, 22.1

autosave, 22.2.33

interactions, 22.2.12

backbone, 22.2.13

ligandbox, 22.5.9

background color, 22.2.2

measure distance ring, 22.8.16

job, 22.5.19

merge, 22.4.5

beep, 22.2.35

modeling, 22.7

binding energy, 22.5.2

molcart 64bit, 22.1.3

blend transition, 22.2.31

query, 22.9.5

breaks, 22.2.34

sdf, 22.9.4

change torsion, 22.4.16

text search, 22.9.6

chem table display, 22.8.4

molecule c, 22.2.5

chemical monitor, 22.8.10

moledit, 22.8.2

query2, 22.8.1

movie planes, 22.2.19

cheminformatics, 22.8

newscript, 22.10.1

clipping plane, 22.2.11

nmr, 22.4.18

closest, 22.4.22

nvidia error, 22.1.2

color carbon, 22.2.4

origin, 22.2.10

skin, 22.2.16

plist, 22.1.9

command line display, 22.2.32

pmf score, 22.5.6

convert chemical from pdb, 22.4.1

pockets, 22.2.14

covalent bond, 22.4.2

preserve coordinates, 22.8.6

delete, 22.4.9

quad buffer, 22.1.7

descriptors, 22.8.15

receptor selection, 22.5.14

deselect, 22.2.7

reload dock, 22.5.4

dihedral, 22.2.18

remove salt, 22.8.14

dock charge groups, 22.5.22

select, 22.2.6

probe, 22.5.13

renumber, 22.4.4

racemic, 22.5.21

residue number selection, 22.2.36

repeat, 22.5.5

rmsd, 22.4.7

working directory, 22.5.23

rmsdtips, 22.4.8

docking, 22.5

rocking active ppt, 22.3.1

docktime, 22.5.11

speed, 22.3.2

scale display, 22.2.38

fitting, 12.11, 17.4.16

scanScoreExternal, 22.5.17

five-membered ring conformation, 5.5.12

scanScoreExternal2, 22.5.18

flexibility, 5.6.5, 12.6.3, 21.12

score, 22.5.8

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

script, 22.10

APF superposition to template, 10.37.4

sequence secondary structure, 22.6.1

docking, 16.13

alignments, 22.6

receptor groups, 16.13

smiles, 22.8.11

ring sampling level, 12.2.1.3

solvent accessible surface table, 22.4.19

flood, 9.22.17

ss, 22.4.17

fog, 3.6.3.5, 6, 6.10.1

structure, 22.4

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

superimpose, 22.4.6

preferences, 4.20.7

surface display, 22.2.37

size, 8.7, 22.1.16, 22.2.1

thoroughness, 22.5.12

form view, 17.1.5

transparent ribbon, 22.2.3

formal, 5.1.3, 22.4.21

truncate mesh, 22.2.15

charge, 6.1.9, 10.15, 10.18

view stack, 22.9.8

format, 17.1.2, 17.1.40

weak hydrogen bonds, 22.4.20

formula, 10.4.9, 10.11

write pdb, 22.4.3

fragment, 10.3.35, 10.36.1, 13, 13.2, 16.11

faqcontour, 22.2.28

linking, 16.11

faqhbondstrength, 22.2.29

screening, 13.2

faqmaps, 22.2.27

fragments, 10.8

faqoda, 22.2.26

frame, 8.3.3

faqstereo, 22.1.14

free energy, 9.13, 9.14

fasta, 8.1.5

radical, 10.4.7

fbdd, 13.2

wilson regression analysis, 10.36.2

fft, 12.13.1

freedomspace, 10.5.5

protein protein docking, 12.13.1

freeze column, 17.1.30

file, 3.6.1.3

row, 17.1.31

close, 3.6.1.13

frequency, 10.3.35

compatible, 3.6.1.10

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

global side-chain sampling, 9.19

hetero, 10.3.28

glutamine proline, 9.22.2

scan, 16.7

google, 3.6.1.7

hidden block format, 8.7.11

objects, 6.3.7

width, 8.7.11

3D, 3.7.6, 6.3.7

hide, 17.1.39

gpcr_model, 21.5.1

column, 17.1.28

graft loop, 9.5

high, 3.6.1.15

graphical, 22.2.4

quality, 3.6.3.11

display, 5.1.3.1, 5.1.3.2, 10.7.2, 10.7.3

highlight new data, 10.3.7.1

tutorial, 21.1

his, 22.4.15

2D3D labels, 21.1.4

histidine, 9.22.2, 22.4.15

annotation, 21.1.2

tautomer, 22.4.15

color representation, 21.1.1

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

labels, 21.1.3

bins, 17.4.3

user interface, 22.2

options, 17.4.2

card, 22.1.2

bin.size, 17.4.2

controls, 6

bins, 17.4.3

defects, 22.1.12

color, 17.4.2

effects, 6.10

source, 17.4.2

panel, 6.2

style, 17.4.2

preferences, 4.20.3

title, 17.4.2

shadow, 3.6.3.13, 6.10.2

historeceptomics, 4.16.9

green arrows, 8.7.16, 22.6.2

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

lines, 8.2, 22.6.1

cluster apf, 13.1.9.5

grid, 10.3.3, 10.37, 21.12.1, 22.8.4

columns, 12.4.3.1

grob, 4.20.5, 5.3.4, 5.3.6, 5.3.7, 6.3

export, 12.4.4

group, 10.36.1, 16.6

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

column, 17.1.46

model, 9.1, 9.1.1.2

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, 5.6.4

find replace, 10.3.13

heatmap, 17.4.7

mark row, 10.3.14

example, 17.4.7.1

markush, 21.6.8

helix, 22.2.20

structure, 21.6.7

help, 2

merge tables, 10.3.23

videos, 2

properties, 10.3.19

reorder, 10.28.3

icb, 4.18.2, 4.19, 22.2.30, 22.3.3

sdf, 10.3.9

icm, 22.3.3

show hide, 10.3.8

chemist howto chemical search, 3.4.3

sort column, 10.3.5

cluster, 3.4.5

standardize, 10.3.18

combi library, 3.4.7

table hyperlinks, 10.3.15

ph4, 3.4.4

print, 10.3.11

plots, 3.4.8

activeicm, 3.3

sketch, 3.4.1

create molecular documents, 3.3.3

spreadsheets, 3.4.2

slides, 3.3.2

stereoisomers tautomers, 3.4.6

getting started, 3.3.1

pro 3D ligand editor, 3.5.1

ppt, 3.3.4

chem3D, 3.5.2

web, 3.3.5

chemsuper, 3.5.4

chemical clusering, 10.28.1

energy, 3.5.3

icm browser convert display pocket, 3.1.4

qsar, 3.5.5

distances angles, 3.1.9

tutorials, 3.5

get started, 3.1.1

tutorials, 3.4

graphical display, 3.1.2

hanging, 22.1.13

effects, 3.1.5

object, 5.1, 21.3.2

images, 3.1.7

script, 17.1.40

labels annotation, 3.1.6

icm-crash, 22.1.13

pro crystallographic tools, 3.2.6

icmFastAlignment, 8.4

get started, 3.2.1

icmPocketFinder, 5.6.7, 22.2.14, 22.5.10

graphics, 3.2.2

icmdb, 19

plots, 3.2.8

icmjs, 7.16

sequence analysis, 3.2.7

icmpocketfinder, 21.3.7

structure analysis, 3.2.3

id, 17.1.27

superimpose, 3.2.5

identity, 4.2.3

surfaces, 3.2.4

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

install, 1, 10.10.1, 19.1, 22.1.3, 22.1.4

2D, 3.7.3

installation, 22.1

3D, 3.7.3, 6.8.1

interaction, 5.5.3, 10.6, 22.2.12

atom, 6.8.1

fingerprint, 13.1.9.6

atoms, 6.8.2

fingerprints, 13.1.9.6

color, 6.8.7

lists, 13.1.10

custom, 6.8.8

restraint, 12.5

delete, 6.8.1, 6.8.9

restraints, 12.5

distance, 6.8.10

interactions, 16.3.12, 22.5.2

drag, 3.6.3.16

interactive, 12.3.1, 21.2

move, 3.6.3.16, 6.8.4

loaded ligand, 12.3.1.2

residue, 6.8.1

loop, 9.1.4.2

residues, 6.8.3

modeling, 9.1.4

site, 6.8.1

table ligand, 12.3.1.1

sites, 6.8.6

modeling, 9.1.4

variable, 6.8.1

interface prediction, 21.10

variables, 6.8.5, 22.2.18

internal hydrogen bonds, 12.1.5

labeling, 6.8.1

internet explorer, 22.3

labels, 6.8, 10.3.28

interrupt, 6.10.7.3

distances, 6.8.10

animation, 6.10.7.3

tab, 3.7.3

introduction, 1

landscape, 4.20.6

invert selection, 17.1.23

large chemical space, 21.6.4

invisible residue label, 22.1.12

font, 22.1.16

ionization, 9.12, 9.12.1

size, 22.1.9

iqr, 17.4.23

sdf, 10.1.2

isee, 7.6.5

layer, 6.14

isis, 10.4.18

layers, 6.14

isostere, 13.4

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

isotope, 10.4.3, 10.5.1

learning, 11

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

environment, 9.19

pocket, 5.2.1, 22.4.11

sequence, 8.1

surface, 16.3.2

extract pdb, 8.1.3

receptor contacts, 16.3.12

from file, 8.1.4

display, 5.2

paste, 8.1.2

interaction, 10.6

swissprot, 8.1.1

strain, 16.3.10

libraries, 9.22.6

surface, 5.2.3

local, 22.2.24, 22.2.25

tether, 16.12

databases, 18

vicinity, 9.19

minimization, 9.19

ligand-based, 13, 13.3

database.browse, 18.2

ligand-induced RNA conformational changes, 5.5.12

edit, 18.3

convert, 9.22.1

query, 18.4

editor, 16, 16.1

row, 18.3

binding.re-dock ligand, 16.9

localpdb, 22.2.24

display, 16.3

localseq, 22.2.25

edit, 16.5

lock, 6.3.10, 6.13.1, 10.3.31

energy, 16.3

log, 17.4.6, 17.4.11

hydrogen.bond, 16.3

logD, 10.11.8

pocket, 16.3

logP, 10.4.9, 10.11

preferences, 16.2

logS, 10.4.9, 10.11

restraint, 16.12

logarithmic, 17.4.11

surface, 16.3

logout, 3.6.1.19

tether, 16.12

loop, 9.3, 9.5, 22.2.20

optimization, 21.11.3

analysis, 9.7

pocket, 4.9

design, 9.4

receptor.contact, 5.5.3

find pdb segments, 9.7

ligand_pocket_interactions, 5.2.1

model, 9.3, 9.4, 21.5.2

ligedit distance restraint, 16.12.2

tutorial, 21.5.2

tab, 3.7.5

modeling, 9.1.4.2, 9.6, 9.7, 9.22.10

tether, 16.12.1

preferred residues, 9.6

light, 3.7.2

model, 9.22.9

tab, 3.7.2

sample, 9.22.9

lighting, 6.3.9.4, 6.5

energy water, 9.22.17

likeness, 10.11, 22.8.9

mac, 10.10.1, 22.1.9, 22.1.16

line, 4.20.5, 17.7.4, 22.2.12

font, 22.1.16

lineWidth, 4.20.3

size, 22.1.16

link, 8.3.9

machine learning, 21.13

structure to alignment, 21.4

macrocycles, 9.21

linker, 12.14

macros, 7.14

links, 4.6.20

macroshape, 3.6.3.22, 6.3, 6.3.6

linux, 10.10.1

make, 6.10.7.1, 17.1.1

lipinski rule, 10.34

alignment, 8.6.1

list, 4.6.18

animation, 6.10.7.1

liver, 10.11.5

apf docking sar model, 15.6

lmhostid, 22.1.18

complex, 13.1.9.4, 16.23

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

flat, 22.8.13

example alignment, 8.3.14

molecular document, 7.6

nmr model, 4.2.5

molt, 18.1

pdb hyperlinks, 4.2.6

receptor maps, 12.2.1.2

protein structure, 5.1.1

selection, 4.6

bond, 22.4.2

save, 6.3.11

disulfide, 9.10, 22.4.17

options, 6.3.9

molecule, 3.6.1.1

meshes, 6.3.2, 6.10.5

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

map, 4.20.7, 5.3.4, 5.3.6, 5.3.7

minimization, 9.18

cel, 5.3.5

cartesian, 9.22.8

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

global, 9.22.8

mark, 17.1.45

local, 9.22.8

row, 17.1.45

minimum specifications, 1

color, 17.4.14

mmff, 9.22.6, 10.4.16, 22.2.17, 22.8.5

shape, 17.4.13

type, 6.8.2

size, 17.4.13

mmp, 21.6.11

markush, 10.28.7, 10.35.1, 10.35.3, 10.36.1, 21.11.3

mnSolutions, 4.20.10

docking, 21.11.3

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

library, 21.6.8

domain interaction, 9.18

mass, 22.4.22

start, 9.1.1.2

matched pair, 10.36.6, 21.6.11

weight, 11.1.4

analysis, 10.36.6

modelers view, 9.1.4.1

materials, 3.7.6

view, 9.1.4.1

max, 17.7.1

modeling, 9.22.3

maxColorPotential, 4.20.10

options, 9.1.1.1

maximum common substructure, 10.28.6, 10.30, 10.30.1

modeller view, 9.1.4

dendrogram, 10.30.1

modification history, 16.5.6

mcs, 10.28.6, 10.30.1

modify, 9.12.2

rgroup decomposition, 10.28.7

amino acid, 9.12

mean, 17.4.6, 17.4.23, 22.4.7

group, 9.11

measure distance, 22.8.16

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

to ring, 22.8.16

mol2, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6

median, 17.4.6, 17.4.23

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

membrane, 12.1.7, 14.3

add database, 10.10.3

exposed docking, 12.1.7

administration, 10.10.5

memory, 10.1.2

connect, 22.9.2

menu, 7.6.5

download dbs, 22.9.3

chemistry, 3.6.14

hostid, 22.9.1

docking, 3.6.15

installation, 10.10.1

homology, 3.6.13

license, 22.1.4

molmechanics, 3.6.16

search, 10.10.4

tools chemical search, 3.6.11

start, 10.10.2

molecular editor, 3.6.12

connect, 22.9.2

windows, 3.6.17

hostid, 22.9.1

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

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, 9.22

zoom, 6.11

convert, 9.22.1

movie, 6.16.1, 22.2.19, 22.9.7

design loop, 9.22.10

montecarlo, 22.9.7

edit structure, 9.22.5

making, 6.16, 6.16.2

gamess, 9.22.16

open, 6.16, 6.16.2

generate normal mode stack, 9.22.14

mpa, 21.6.11

his asn, 9.22.2

mpeg, 6.16, 6.16.1, 6.16.2

ic table, 9.22.13

mpg, 6.16, 6.16.2

impose conformation, 9.22.4

mpo, 10.34

minimize, 9.22.8

binary classification, 10.34.2

mmff, 9.22.6

custom step function, 10.34.1.2

regularization, 9.22.3

customized, 10.34.1

sample loop, 9.22.9

save, 10.34.1.3

peptide, 9.22.12

special cases, 10.34.1.1

protein, 9.22.11

mtl, 6.7

terms, 9.22.19

multi apf super, 10.37.7

view stack, 9.22.15

panel, 6.2

modeling, 9, 9.19

parameter optimization, 10.34

table, 10.20.2

template, 9.1.4.3

weight, 10.4.9

windows, 6.2

molecule, 22.2.8, 22.8.3

multiple, 12.6.2, 21.12.1

editor, 10.4

chain, 9.1.2.2, 9.1.3.1

moledit, 10.4.8

position group scan, 16.7

molmechanics, 22.9.8

rec, 12.6.2

minimize, 9.22.8

receptor, 4.16.1, 21.12

mmff, 9.22.6

docking, 16.15

molscreen, 13, 15

protein, 22.2.5

custom model panel, 15.4

mutant, 9.11, 22.4.13, 22.4.14

load models, 15.1.1

mutate, 9.13, 9.14, 22.4.15

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, 10.11.7

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

nephrotox, 10.11.4

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

neural network, 12.4.3.1, 16.18

column, 17.1.28

Torsion Profile Neural Network Prediction Engine, 6.12.6.1

mesh, 6.3.9.2

new, 8.1

slide, 7.4.2

icm session, 3.6.1.2

structure, 6.12

table, 17.1.1

nmr, 22.4.18

pages, 19.7

model, 4.2.5

pairwise, 10.37.5, 10.37.6

nnc, 15.3.5

apf score, 10.38

nntorsion, 6.12.6.1

parallelization, 13.1.7

nof, 10.11.2

password, 10.10.5

chemical, 10.11.2

paste, 10.4.11, 10.4.18, 17.1.35

non-contiguous selection, 4.6.18

pca, 17.5

normal modes, 9.22.14

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

nucleic acid conformation analysis, 5.5.12

chem gl, 10.7.3

geometry, 5.5.12

iw, 10.7.2

nucleotide analysis, 5.5.12

dormat, 4.19

conformation, 5.5.12

file, 22.4.3

geometry, 5.5.12

html, 4.2.7

puckering, 5.5.12

preparation, 21.3.11

number of sp3, 10.11.2

search, 4.2.3, 4.2.4, 21.3.1

numbers, 10.3.28

hyperlinks, 4.2.6

nvidia, 22.1.2

convert, 9.22.1

obj, 6.7

recent, 3.6.1.18

object, 4.12, 4.19, 21.3, 22.2.8

search, 3.7.4, 4.2, 4.2.1

objects, 5.1.2

pdbsearchfield, 3.6.2.13

in table, 17.3

pdbsearchhomology, 3.6.2.15

in.table, 17.3

pdbsearchidentity, 3.6.2.14

occlusion, 6.3.12, 6.10.5

pdbsearcsequence, 3.6.2.16

shading, 6.3.12

peptide, 4.17, 9.15, 9.21, 12.12

effect, 6.10.5

docking, 12.12

occupancy, 6.1.3, 21.3.10

modeling, 9.21

oda, 5.6.6, 12.13, 12.13.2, 12.13.3

editor, 16.21

older version, 3.6.1.10

percentage similarity, 8.7.15, 21.4.4

omega, 6.8.5, 22.2.18

perspective, 3.6.3.9, 6.10.6

online databases, 10.5.5

ph4, 10.5.6

open, 3.6.1.3, 4.18, 17.1.2

draw 2d, 10.5.6.1

file, 4.18

3d, 10.5.6.2

password, 4.18.1

search, 10.5.6.3

with password, 3.6.1.4

pharmacophore, 10.3.35, 10.5.6.5, 21.8.2

movie, 6.16, 6.16.2

2D, 21.6.6

password, 3.6.1.4, 4.18.1

3D, 21.6.5

optimal, 5.6.6, 12.13, 12.13.2, 12.13.3

clone, 10.5.6.2

optimize, 9.22.2

draw2D, 10.5.6.1

oracle, 19

draw3D, 10.5.6.2

orange, 4.6.5

edit, 10.5.6.1, 10.5.6.2

selection, 4.6.5

move, 10.5.6.2

origin, 6.8.12, 22.2.10

new, 10.5.6.2

orthosteric, 5.6.7

search, 10.5.6, 10.5.6.3, 21.6.5, 21.6.6

other selection, 4.6.19

phase angle P, 5.5.12

outside, 22.5.9

phi, 6.8.5, 22.2.18

overlay, 21.3.3, 22.2.5, 22.4.6

phylogenetic, 8.7.8

pH, 5.6.2, 10.19

phylogeny, 8.7.8

pKa, 5.6.2, 9.12, 9.12.1

physics-based score, 12.4.3.1

package.activeicm, 7.13

pi, 5.2.5

packing, 5.3.1

cation, 5.2.5

picking, 6

potential mean force, 13.1.4

picture, 3.6.1.14, 4.15, 6.15.2, 7.6.3

ppbatch, 12.13.9

tips, 4.15

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

planar, 5.5.7, 6.8.5, 22.2.18

pproc, 12.13.3

angle, 5.5

ppsetligand, 12.13.6

angle, 6.9.2

ppsetproject, 12.13.4

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

ppsetreceptor, 12.13.5

faq, 22.2.21

ppt, 7.12, 7.14, 22.3.3

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

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

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

function, 3.6.9, 3.6.9.1

prediction binding, 9.13

grid, 17.4.15

preferences, 4.20, 13.1.5, 22.2.24, 22.2.25

header, 17.4.9

preferred residues, 9.6

inline, 17.4.22

presentation, 7.6.5, 7.7, 7.12

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, 4.20.8

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

zoom translate, 17.4.17

print, 6.7, 17.4.20, 17.7.3

axis, 17.4.15

alignment, 8.7.4

display, 17.4.15

plot, 17.4.20

grid, 17.4.15

alignment, 8.7.4

inline, 17.4.22

printer.resolution, 4.20.6

logarithmic, 17.4.12

pro-drug, 10.26

pls, 10.21, 10.22, 11, 17.6, 21.13

probe, 12.2.1.1, 22.5.13

pmf, 22.5.6

problem, 22.1.14

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, 5.6.7, 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, 5.6.7

expression, 13.1.9.4

point label, 17.4.19

monitor, 10.4.9

portait, 4.20.6

protac, 12.14

post edit ligand, 16.5.8

protect, 7.6.8

screen, 13.1.9

protein, 5.4.6, 8, 9.15, 22.4.5

postscript, 4.20.6

chain, 9.4

model, 9.20

analysis, 5.5.12

preparation, 9.12, 9.12.1

phase angle, 5.5.12

protein docking, 21.10

psi, 6.8.5, 22.2.18

tutorial, 21.10

pubchem, 10.1

sculpting, 9.18

publication quality images, 6.3.2

sequence, 10.4.17

puckering amplitude, 5.5.12

structure, 5

purple box, 3.6.3.23, 12.2.1.1, 16.9.1

analysis, 5.5

pyramid, 12.1.6

closed cavities, 5.5.4

pyramidal, 12.1.6

contact areas, 5.5.3

qs hydrogen bond, 5.2.4

distance, 5.5.6

pdb chem gl, 5.1.3.2

find related chains, 5.5.1

iw, 5.1.3.1

finding dihedral angle, 5.5.8

qsar, 10.21, 10.22, 11.1, 21.13

planar angle, 5.5.7

learn predict, 10.21

rama export, 5.5.10

predict, 10.22

ramachandran plot, 5.5.9

quad buffer stereo, 22.1

rmsd, 5.5.2

buffer, 22.1.7

surface area, 5.5.5

quality, 3.6.1.15, 4.20.5

similarity, 5.7

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

tutorials, 21.3

molt, 18.4

analysis, 21.3.4

processing, 10.5.3

contact area, 21.3.5

setup, 10.5.1

convert, 21.3.2

quick, 4.15

hydrogen bond, 21.3.6

image, 6.15.2

icmpocketfinder, 21.3.7

model multiple chain, 9.1.2.2

search, 21.3.1

single chain, 9.1.2.1

superimpose, 21.3.3

start move structure, 4.4

superposition, 5.4

read pdb, 4.2

select, 5.4.1

representation, 4.7

sites by apf, 5.4.6

what is selected, 4.6.4

superimpose 3D, 5.4.3

display.distance, 6.9.1

grid, 5.4.5

start color, 4.8

multiple proteins, 5.4.4

quit, 3.6.1.19

protein-ligand complex, 9.19

group, 10.28.7, 10.35.4

protein-protein, 5.6.6, 12.13, 12.13.1, 12.13.2, 12.13.3, 12.13.4, 12.13.5, 12.13.6, 12.13.8, 12.13.9, 12.13.10, 21.10

table, 10.35.2

docking refinement, 12.13.11

groups, 10.35.2

protein-proteindocking, 12.13.7

r-group, 10.28.7, 10.35.2

convert, 9.22.1

decomposition, 10.28.7

protonated, 22.4.15

enumeration, 10.28.7

protonation, 9.12, 9.12.1, 10.19, 12.1.4

r-groups, 17.4.25

charge, 9.12.1

racemic, 10.3.28, 10.20.5, 22.5.21

state, 12.1.4

radar, 17.4.6

states, 5.6.2, 9.12, 9.12.1

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, 10.11.9

dock ligand, 16.9

pseudorotation P, 5.5.12

reactions, 10.8, 10.35.5

reactivity, 10.11.3

representation, 3.6.3.19

read, 3.6.1.3, 3.6.1.17, 4.18, 8.1, 10.3.1

residue, 4.20.7, 22.2.8, 22.4.15, 22.4.22

chemical, 10.1

alternative orientation, 21.3.11

spreadsheet, 10.3.1

content, 8.3.1

split, 11.1.1

names, 9.12, 9.12.1

table, 17.1.2

number selection, 22.2.36

pdb, 4.2, 4.2.1

pKa prediction, 5.6.2

table, 17

pka, 5.6.2

reagent, 10.35.5

range, 4.6.18

rear, 6.3.10, 6.13.1

content, 3.6.4, 8.3, 8.3.1

recent files, 3.6.1.17

mutate, 22.4.13, 22.4.14

pdb codes, 3.6.1.18

residues, 5.2.2, 5.2.3, 22.2.14

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

resize, 6.3.9.1, 6.15.3

considerations, 12.1.1

mesh, 6.3.9.1

flexibility, 16.15

resolution, 4.2.4

pocket, 16.3.1

restore, 3.6.2.11, 6.3.10, 6.13.1

surface, 16.3.1, 16.3.2

default, 22.1.9

refinement, 9.19

recent backup, 3.6.2.11

flexibility, 21.12.2

restrained docking, 12.5

recover, 3.6.2.11

restraint, 16.12.1, 16.12.2

cylinders, 8.7.16, 22.6.2

restraints, 14.2

lines, 8.2, 22.6.1

results, 12.13.10

redo, 3.6.2.10, 10.4.11, 16.5.5

stack, 12.4.2

refine, 9.8, 9.9

retrieve columns, 22.5.24

loops, 9.1.3

from original database, 22.5.24

side chain, 9.9

review and adjust binding site, 12.2.1.1

sidechains, 9.1.3

rgroup, 10.35.4

refinement, 12.6.4

ribbon, 3.7.1, 4.20.9, 6.1.3, 22.2.23, 22.2.34

region, 12.13.7

as a mesh object, 22.2.3

regression, 10.36.2, 11.1, 11.5, 17.4.16, 21.13

faq, 22.2.23

regul, 9.8

preferences, 4.20.9

regularization, 9.8, 9.22.3

style, 4.20.9

relationship, 11, 17.6

breaks, 6.1.3

covalent geometry, 12.2.1.3

cylinders, 6.1.3

relaxed ligand, 16.3.9

smooth, 6.1.3

reload, 12.4.5, 22.5.4

worm, 6.1.3

dock results, 12.4.5

ribbonColorStyle, 4.20.9

remove, 22.2.6, 22.2.7, 22.2.10

ribose pseudorotation, 5.5.12

salt, 22.8.14

pucker, 5.5.12

explixit.hydrogens, 10.12

ring, 5.5.12

salt, 10.12

conformation, 5.5.12

rename, 17.1.25

torsion angles, 5.5.12

column, 17.1.25

ride, 13.4

project, 3.6.1.9

gpu benchmark, 13.4.1.2

renumber, 9.2, 22.4.4

server setup, 13.4.1.1

reorder column, 17.1.29

setup, 13.4.1

replace chemical, 10.3.32

ridge, 13.5

replacement, 16.6

right, 4.13

group, 16.8

click, 4.13

report, 19.3

rigid, 10.37

ring, 5.2.5, 10.4.3, 10.4.6, 10.5.1

file, 4.19

stacking, 5.2.5

hits, 16.5.7

rings, 10.3.28, 10.23, 10.37

image plot, 17.4.21

rmsd, 5.5, 5.5.2, 22.4.7, 22.4.8

ligand receptor complex, 16.20

rock, 3.6.3.15, 6.10.7, 6.10.7.1, 7

object, 4.10

speed, 6.10.7.2

pdb, 4.19

root, 22.4.7

project icb, 4.11

mean square deviation, 5.5.2

sequence, 8.1.5

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

slide, 7.4

chemical, 10.3.34

smiles string, 10.4.15

torsion, 6.12.6.1

table, 17.1.21

when pasting, 10.4.8

spreadsheet, 16.5.7

easy, 3.6.3.12

tree, 17.7.3

speed, 6.10.7.2

sdf, 10.4.14

rotating fragment in editor, 10.4.8

image, 3.6.1.15, 4.15

rotation, 6.12.1

object, 4.10

rotational symmetry axis, 5.5.11

password, 3.6.1.11

rough surface, 22.2.37

picture, 3.6.1.15

row, 17, 17.1.22, 17.1.35, 17.1.45

project, 3.6.1.8, 3.6.1.9, 3.6.1.10, 4.11

flag, 17.1.13

table.view, 17.1.8

height, 17.1.7, 22.2.39

saving, 3.6.1.8

mark, 17.1.13

project, 3.6.1.8

hide, 10.3.8

scaffold, 10.14

show, 10.3.8

hopping, 16.8

ruler, 6.8.16

scale, 4.20.5, 22.2.38

molscreen, 15.1.2

scan, 9.22.7, 12.4.1

rundock, 22.5.16

hits, 12.4.1

rxn, 10.4.13

group, 16.7

safari, 22.3

scan_pockets, 5.8

sali, 10.36.5

scarab, 19

bridge, 21.3.6

add user, 19.5

salts, 10.3.18

browse export data, 19.4

sample, 9.20, 10.37

installation, 19.1

double bond cis trans, 12.2.1.3

new project, 19.6

ligand pocket, 9.19

pages, 19.7

peptide, 9.21, 9.22.12

query, 19.3

protein, 9.20, 9.22.11

upload data, 19.2

racemic centers, 12.2.1.3

scare, 12.6.4

sar, 10.28.7, 10.36, 17.4.25

scatter, 13.1.9.2

analysis, 10.36

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

table, 10.36.3

threshold, 13.1.4

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

screen, 10.38, 21.8.4, 21.9, 21.11.1

SMILES, 10.4.15

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

alignment, 8.7.3

screenshot, 6.16, 6.16.2

PDB, 4.19

movie, 6.16.2

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, 16.20

chembl, 4.16.2

filter, 10.5.2

invert, 3.6.2.6, 17.1.23

in workspace, 3.6.2.4

level, 3.6.3.3

pdb, 4.2.1

mode, 3.6.3.4

ligand code, 4.16.6

near atoms, 3.6.2.8

pocketome, 4.16.1

neighbors, 3.6.2.5, 3.6.2.8, 4.6.15, 4.6.17

pubchem, 4.16.8

object, 4.6.11

surechembl, 4.16.3

other, 4.6.19

tab field, 4.2.4

properties, 3.6.2.5

pdb chemical, 4.2.2

range, 17.1.23

sequence, 4.2.3

residue, 3.6.2.5

tautomer, 10.5.3

row, 17.1.23

uniprot, 4.16.5

sphere, 4.6.15

in.workspace, 3.6.2.4

spherical, 3.6.2.8

secondary aliphatic amines, 10.15

superposition, 5.4.1

structure, 5.6.1, 22.2.20

table, 4.6.19, 17.1.23

structure, 3.6.4, 6.1.3, 8.3, 8.3.2

elements, 17.1.23

select, 4.6.12, 4.6.13, 17, 17.1.45, 22.4.22

tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8

a tree branch, 17.7.2

whole, 4.6.11

all, 4.6.14

workspace, 4.6.9, 4.6.17

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, 4.2.3, 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

residue, 4.6.13, 4.6.18

analysis, 8.3

by number, 4.6.18

editor, 8.5

number, 4.6.18

identity, 8.7.15

tree, 17.7.2

pattern, 4.2.3

atom, 4.6.3

reordering, 8.7.8

graphical, 4.6.3

secondary structure, 8.2, 22.6.1

object, 4.6.3

similarity, 8.7.15

purple.box, 3.6.3.23

sites, 8.5

residue, 4.6.3

structure, 8.3.6

workspace, 4.6.3

type, 8.3.4

selectall, 3.6.2.3

DNA, 8.3.4

selecting.neighbors, 4.6.16

alignment, 8.3.5, 8.6.2, 8.6.6

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

structure.alignment, 8.3.6, 8.6.3

alter, 4.6.7

sequences, 8, 22.2.25

atom, 3.6.2.5

unique, 8.3.13

basic, 4.6.2

extract, 8.3.13

change, 4.6.7

unique, 8.3.13

clear, 3.6.2.7

server, 13.1.7.2

column, 17.1.23

error, 22.1.17

filter, 3.6.2.5, 4.6.8

set, 10.3.31, 22.4.21

graphical, 4.6.16

formal charges, 10.15

bond type, 9.22.5

slice, 6.13

charges, 9.22.6

slide, 6.10.7.4, 7.2, 7.3.1, 7.6.1, 22.2.31

chirality, 9.22.5

effects, 7.5

disulfide, 9.10, 22.4.17

movie, 6.16.1

bond, 9.22.5

file, 7.2

formal charge, 9.22.5

navigation, 7.3.2

tether, 9.22.5

show, 7.3

types, 9.22.6

blend, 7.5

setAPFparams, 22.8.12

edit, 7.4.1

setup, 12.13.6

effect, 7.5

ligand receptor, 16.1

smooth, 7.5

shade, 8.7.7, 8.7.7.1

transition, 7.5

alignment, 21.4.4

slides, 6.16.1, 7, 7.1, 7.3, 22.2.30

shading, 6.3.12

smiles, 10.4.9, 10.11, 10.20, 10.20.3, 10.20.4

shadow, 6.10.2

smooth, 6.3.9.3

share model, 11.1.5

surface, 22.2.37

sheet, 22.2.20

solid, 6.3.9.3

shell preferences, 4.20.10

solvent.accessible.area, 22.4.19

shift, 6.8.3

sort hitlist, 13.1.9.1

shine, 3.7.2, 4.20.5

table, 3.6.10.4

shineStyle, 4.20.3

sorting, 13.1.9.1

show, 7.3.1, 17.1.39

compounds, 17.7

hide column, 17.1.39

sp3, 10.11.2

side, 10.3.29

spec, 3.7.2

by side, 10.3.29

specifications, 22.1.5

error, 22.1.19

specs, 1

stereo, 3.6.3.6

faq, 22.1.5

chain refinement, 16.14

speed, 6.10.7.2

chains, 9.9

sphere, 22.4.11

side-by-side, 22.1.19

spherical, 22.4.9, 22.4.12

side-chain optimization, 9.19

split, 10.36.1

sampling, 12.13.11

spreadsheet, 10.20.2

side-chains, 12.6.1

square, 22.4.7

sigmaLevel, 5.3.6, 5.3.7

stability, 9.14, 21.5.3, 21.5.4

similarity, 10.31

stack, 9.20, 9.22.18, 12.4, 12.13.10, 22.9.8

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

calculations, 9.22.18

length, 22.5.12

stacking, 5.2.5

simulations, 22.7

standalone hitlist, 12.4.4

single, 10.4.10

standard table, 17.1

chain, 9.1.2.1

standardize, 10.12

singlet, 10.4.7

table, 10.12

sites, 5.4.6

start, 10.10.2

size, 5.2.4.1

startup, 22.10.2

sketch accents, 6.10.3

static, 22.4.8

markush, 10.35.1

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

reaction, 12.8.1

bond, 10.4.2

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

stick, 4.20.5

clone, 17.1.16

stl, 6.7

color, 17.1.10

stop, 6.10.7.3

column format, 17.1.40

store, 3.6.3.19, 6.10.7.4, 22.2.22

copy, 17.1.36, 17.1.37

current view, 3.6.3.19

delete, 17.1.17

faq, 22.2.22

edit, 17.1.24

strain, 5.6.4, 6.12.6.1, 10.17, 10.27, 10.27.2, 12.1.10, 12.4.3.1, 16.4

filter, 17.1.43

strip, 22.4.9

find, 17.1.9

structure, 5.3.3, 11, 17.6, 21.3, 22.4

replace, 10.3.32

analysis, 5.5.12, 21.3.4

font, 17.1.11

ensemble, 9.22.14

size, 22.2.1

preparation, 9.19

grid, 17.1.5

representation, 6.1

histogram, 17.4.1

smiles, 10.20.4

insert, 17.1.26

structure-based, 13

layout, 17.1.5

structures, 10, 10.1

learning, 17.6

style, 4.20.5

mark, 17.1.13

substituent, 10.9.1, 10.9.2, 10.35.2, 16.5.2

row, 17.1.13

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

mouse, 17.1.47

template, 16.12.3

navigation, 17.1.4

alerts, 10.13

new column, 17.1.26

sugar conformation, 5.5.12

plot, 17.4

pucker analysis, 5.5.12

print, 17.1.19

puckering, 5.5.12

rename, 17.1.15

ring puckering, 5.5.12

rightclick, 17.1.14

sulfur, 9.10

row height, 22.2.39

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

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

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

view, 17.1.5

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

save, 17.1.8

area, 5.5

zoom translate, 10.3.30

area, 5.5.5

action, 17.1.47

surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5

alignment, 17.1.12

surrounding, 22.4.11

append, 17.1.43

swissprot, 8.1, 8.5

clone, 17.1.16

sxstrace, 22.1.19

color, 17.1.10

symmetric oligomer, 9.1.3

column, 10.3.4, 17.1.26, 17.1.32, 17.1.39

symmetry, 5.3.1, 5.3.3, 21.3.8, 21.3.9

columns, 10.3.8

synthesize, 10.11.7

compare, 10.3.22

synthetic feasibility, 10.11.7

copy, 10.3.6

system preferences, 4.20.11

cursor, 17.1.47

tab, 17.1.2, 17.1.21

delete, 17.1.14, 17.1.17

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

filter, 10.3.12, 17.1.43

search, 10.5.4

find-replace, 10.3.13

texture, 3.7.6

to screen, 17.1.4

thoroughness, 10.23, 10.37, 22.5.12

font, 17.1.11

three, 10.3.24, 22.8.6

foreground, 22.10.4

threshold, 4.20.5

grid lines, 17.1.4

tier, 4.14

hide, 17.1.39

time, 22.5.11

hyperlink, 10.3.15

machine, 22.1.15

insert, 17.1.33

tissue, 4.16.9

join, 3.6.10.5

racemic, 10.20

label, 10.3.14

tools 3D, 3.6.6

landscape, 17.1.18

analysis, 3.6.7

mark, 10.3.14

append rows, 3.6.10.7

merge, 3.6.10.5, 10.3.23, 10.32

extras, 3.6.9

mouse, 17.1.47

plot function, 3.6.9.1

name, 17.1.15

superimpose, 3.6.8

new, 17.1.1

table, 3.6.10

options, 17.1.14

Learn, 3.6.10.1

orientation, 17.1.18

clustering, 3.6.10.3

portrait, 17.1.18

merge, 3.6.10.5

print, 10.3.11, 17.1.4, 17.1.19

predict, 3.6.10.2

read, 17.1.2

tooltip, 17.4.26

rename, 17.1.15

balloons, 17.4.26

right click, 17.1.14

torsion, 6.12.6, 6.12.6.1, 9.22.7, 10.17, 16.5.4, 22.4.16

row, 17.1.33

analysis, 10.16

rows, 3.6.10.7

angles, 6.12, 6.12.6

save, 10.3.9, 17.1.3, 17.1.4, 17.1.21

free strain, 10.17

scale, 17.1.18

scan, 9.22.7

scroll, 17.1.4

toxscore, 10.11.3

sdf, 10.3.9

trace, 6.1.10

select, 17.1.23

transition.blend, 22.2.31

setup, 17.1.18

transitions, 7, 22.2.30

sort, 3.6.10.4, 10.3.5, 17.1.42

translate, 4.4, 6, 6.12, 10.3.30

standard, 17.1

translation, 6.12.3, 8.3.3, 17.4.17

view, 10.3.29

transparent, 6.3.9.3

width, 17.1.4

background, 6.15.3

tables, 10.31, 17

ribbon, 22.2.3

tag, 4.6.21, 16.5.7, 17.1.46

surface, 22.2.37

tags, 4.6.21

tree, 8.7.8, 10.28.7, 17.7.2, 17.7.3, 17.7.4

m, 5.5.12

branch swapping, 8.7.8

tautomer, 10.24, 22.4.15

distance, 10.28.3

tautomers, 10.24

edit, 10.28.4

temperature, 5.6.5

reorder, 10.28.3

template, 9.1.2, 10.4.6, 10.37

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

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

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, 9.22.15

sequence conservation, 21.4.3

virtual, 13.1, 13.1.1, 13.1.2, 21.9, 21.11.1

tutorials, 21

ligand screening, 15

two, 10.3.24, 22.8.6

screen, 13.3, 13.4

ubuntu, 22.1.18

screening, 13, 13.2

ultra large library, 13.5

examples, 21.11

unclip, 6.3.10, 6.13.1

virus, 5.3.3

undisplay, 4.5, 6.1.7, 22.2.10, 22.2.32

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

undo, 3.6.2.9, 4.20, 10.4.11, 16.5.5

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

uniprot, 4.16.5, 8.5

display, 13.1.9.3

unique, 10.3.28, 10.33

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, 4.17

results, 13.1.8

upload, 19.2

run, 13.1.6

use activeicm, 7.12

score, 12.1.9

user, 10.10.5, 19.5

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

water, 9.22.17, 12.1.8

van der waal, 6.8.15

waters, 9.22.17

variable, 4.20.7, 22.2.8

wavefront, 3.7.6, 6.3.11, 6.7

verbose, 10.23

weak, 22.4.20

large sdf files, 10.1.2

web, 21.2

vicinity, 10.23

browser, 3.6.1.12

video, 2, 6.16, 6.16.1, 6.16.2

weight, 10.11, 22.8.7, 22.8.10

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

wire, 3.7.1, 4.20.5, 6.1.1, 22.2.4, 22.2.21

wireBondSeparation, 4.20.1

working directory, 22.5.23

workspace, 4.5, 5.1.3.1, 10.7.2

panel, 4.5

selection, 4.6.9

navigation, 4.6.10

write, 4.15, 4.19, 17.4.21, 22.9.4, 22.9.7

alignment, 8.7.3

excel, 10.2.3

image, 3.6.1.15, 22.1.20

images, 6.15

pdb, 4.19

image, 3.6.1.15

object, 4.10

picture, 3.6.1.15

project, 3.6.1.8, 4.11

table, 17.1.3

writing a pdb file, 22.4.3

ray, 3.6.5

xi, 6.8.5, 22.2.18

xls, 10.2.3

xlsx, 10.2.3

xml, 19.2

xstick, 6.1.2, 22.2.21

xyz, 22.2.10

youtube, 2

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

τm, 5.5.12