ICM User's Guide: Index

modify group, 9.13.2

Acetyl Cap, 17.21

200 steps, 9.8.2.1

ActiveICM, 3.6.1.12

2025, 9.8.7

Alignment mode, 5.6.11

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

Alpha-Helix Stabilization, 17.21

Chemical Label, 6.8.11

Altona-Sundaralingam pseudorotation, 5.6.12

Interaction Diagram, 17.3.7

Area, 9.23.18, 23.2.26

bioisostere, 10.9.1

Atom Single Style, 4.20.3

chemical label, 6.8.11

Atomic Property Fields, 11.4, 22.14

from PDB, 10.1.1

B3LYP, 15

interaction diagram, 10.6

Bad Groups, 23.8.7, 23.8.10

screening, 16

Baell, 10.4.9

to 3D, 10.20, 10.20.3

Beep, 4.20.11

depiction, 10.20.2

Beta-Catenin, 17.21

3D, 6.6, 6.8.8, 10.1.3, 10.3.24, 10.3.28, 10.3.31, 10.20.2, 22.2

Bioactive Conformation, 17.21

QSAR, 10.38.4, 11.4, 22.14

Blast, 23.2.25

chemical, 10.4.16, 10.20.1

BlastDB Directory, 4.20.2

interactive ligand editor, 3.7.5

alphas, 6.8.3

ligand editor, 17.3.4

C-alpha backbone, 5.6.11

object, 6.3.9

C2′-endo pucker, 5.6.12

pharmacophore, 13.3, 17.3.11

C3′-endo pucker, 5.6.12

print, 6.7

CHEMRIYA, 13.5

printing, 6.7

COLLADA, 3.6.1.7

screening, 16

CPK, 3.7.1

stereo, 6.6

CYM, 9.13, 9.13.1

visualization, 5.6.11

CYS, 9.13, 9.13.1

3DMOLT, 19.5

ChEMBL, 4.16.2, 10.1

3DQsar, 11.4

Chemical Cluster, 22.6.3

3D_Similarity_PDB_Search, 5.8

Search, 22.6.2

3Dqsar tutorial, 22.14

CisTransAmide Angle, 13.1.9.4

3d, 5.3, 5.3.1

Clash Threshold, 4.20.10

bioisostere, 10.9.2

Computational Chemistry, 17.21

predict, 5.7

Computer-Aided Drug Discovery (CADD), 17.21

helices strands, 5.7.1

Covalent Geometry., 17.21

local flexibility, 5.7.5

DFT, 15

protein health, 5.7.4

DILI, 10.11.5

tools identify ligand binding pocket, 5.7.7

DNA, 4.17, 8, 8.3.3

oda, 5.7.6

Decomposition, 10.36.3

4D, 12.6.2, 22.12.1

Design Evolution, 12.10

dock, 17.15

Dimer, 5.6.11

docking, 4.16.1

Display, 23.2.26

6-31G*, 15

Distance, 13.1.9.4

64, 23.1.3

Dock Directory, 4.20.2

A-form RNA, 5.6.12

Docking, 23.2.26

AI, 12.10

Drug Bank, 4.16.7

APF, 10.37.4, 10.37.7, 10.38.4, 11.4, 16, 16.6, 22.14

Design, 17.21

template, 10.37.3

Editor, 4.20.2

ARG, 9.13, 9.13.1

Eintl, 12.1.10

ARN, 9.13, 9.13.1

Error in saving configuration settings: You are not a license administrator, 23.1.10

ASP, 9.13, 9.13.1

Extended Amino Acids, 17.21

ASPH, 9.13, 9.13.1

FILTER.Z, 4.20.2

uue, 4.20.2

lightPosition, 4.20.3

FTP.createFile, 4.20.11

mapLineWidth, 4.20.3

keep File, 4.20.11

occupancy Radius Ratio, 4.20.3

proxy, 4.20.11

occupancyDisplay, 4.20.3

Filter.zip, 4.20.2

quality, 4.20.3

Flexible Minimization, 17.21

rainbow Bar Style, 4.20.4

Force Auto Bond Typing, 4.20.11

resLabelDrag, 4.20.7

Formula, 23.8.7, 23.8.10

resize Keep Scale, 4.20.3

Free Wilson, 10.36.2

ribbonRatio, 4.20.9

Frequently Asked Questions, 23

ribbonWidth, 4.20.9

GAMESS, 9.23.16

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, 9.13, 9.13.1

Speed, 4.20.4

GLUH, 9.13, 9.13.1

selectionStyle, 4.20.3

GPCR Modeling Example, 22.5.1

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, 23.2.33

fontColor, 4.20.7

autoSaveInterval, 23.2.33

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, 19.5

hydrogenDisplay, 4.20.1

Guide to the Hitlist Columns, 12.4.1.1

light, 4.20.3

HBA, 13.1.10, 23.8.7, 23.8.10

HF, 15

InChi, 10.3.20, 10.4.12, 10.20.3

HID, 9.13, 9.13.1

key, 10.3.20

HIE, 9.13, 9.13.1

Interaction Diagram 2D, 17.3.7

HIP, 9.13, 9.13.1

Interactive Ligand Editor, 17.21

HIS, 9.13, 9.13.1

Plot, 5.6.12

HTTP.proxy, 4.20.11

Internal Coordinates Table, 9.23.13

support Cookies, 4.20.11

Directory, 4.20.2

user Agent, 4.20.11

JPEG, 3.6.1.15

Hartree-Fock, 15

KMZ, 3.6.1.7

Hbond to selection, 13.1.9.4

LCC, 13.5

Hbonds, 17.3.4

LYN, 9.13, 9.13.1

Helicon Peptide, 17.21

LYS, 9.13, 9.13.1

Homodimer, 5.6.11

LigStrain, 17.21

Homologous chains, 5.6.11

Ligand Strain, 17.21

To Guide, 3

Liver Toxicity Models, 10.11.5

Html, 4.2.7

Log Directory, 4.20.2

Http Read Style, 4.20.11

LogP, 11, 18.6

Hydrocarbon Staples, 17.21

LogS, 11, 18.6

Hydrogen.bond, 4.20.5

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

I+4 Staple Position, 17.21

Q and A, 14.5

Staple Position, 17.21

MOL, 10, 10.3.3, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 13.1.3, 18.2

ICM, 15

MOL2, 13.1.3

Browser How To, 3.1

MOLT, 19.1

Pro How To, 3.2

MOVIE.frame Grab Mode, 4.20.4

analysis tools, 5.6.12

MPO, 10.34

graphics crash, 23.1.11

Mac, 23.1.15

object, 5.7.2, 9.20

Atom Margin, 4.20.10

start, 1

Sigma Level, 4.20.10

ICM-Pro Tutorial, 17.21

Markush, 22.6.9

IMAGE.bondLength2D, 4.20.6

create, 22.6.7

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, 9.13

lineWidth2D, 4.20.6

MolCart, 23.9

orientation, 4.20.6

MolIPSA, 23.8.7, 23.8.10

paper Size, 4.20.6

MolLogP, 23.8.7, 23.8.10

previewResolution, 4.20.6

MolLogS, 23.8.7, 23.8.10

previewer, 4.20.6

MolPSA, 10.11

print, 4.20.6

MolScreen, 16

printerDPI, 4.20.6

MolSoft ICM-Pro, 17.21

scale, 4.20.6

MolVol, 10.11

stereoAngle, 4.20.6

Molcart, 10.5.3

stereoBase, 4.20.6

MoldHf, 10.11, 23.8.7, 23.8.10

stereoText, 4.20.6

Molecular Docking, 17.21

INCHI, 10.20.3

Dynamics, 14.5

IQR, 18.4.6

Preparation, 17.21

ISIS, 23.8.3

Movie.fade Nof Frames, 4.20.4

Icm Prompt, 4.20.10

quality, 4.20.4

Multimer, 5.6.11

PNG, 3.6.1.15, 4.15, 6.16, 6.16.2

NCBI, 23.2.25

PROPKA, 5.7.2

NH2 Cap, 17.21

PROTAC, 12.14

NVIDIA, 23.1

PSA, 10.11.9

Natural Amino Acids, 17.21

Peptide Engineering, 17.21

NephroTox, 10.11.4

Mode, 17.21

Nof_Atoms, 10.11

Modeling, 17.21

Nof_Chirals, 10.11

Stapling, 17.21

Nof_HBA, 10.11

Pharmacophore RMSD, 13.1.9.4

Nof_HBD, 10.11

PowerPoint, 22.2, 23.3

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, 23.2.26

North conformation, 5.6.12

complex, 5.6.11

Nvidia GL failutre, 23.1.11

Protein-Peptide Interactions, 17.21

ODA, 23.2.26

Viewer, 4.20.2

Optimal, 23.2.26

Pseudorotation Interactive Plot, 5.6.12

Output Directory, 4.20.2

Psi4, 15

PAINS, 10.4.9, 10.11.3

Pub Chem, 4.16.8

chemicals, 10.4.9

PubMed Reference, 18.1.40

PCA, 11.1, 11.5, 22.6.4

Pubchem, 4.16.8

analysis, 10.29

QSAR, 11, 11.1, 18.6, 22.14

PDB, 4.2.7, 5.1.2, 5.4.3, 5.8, 8.1, 10.1.1, 17.20

R, 10.8, 10.36.1

7UWI, 17.21

and S, 23.5.21

Directory, 4.20.2

R-Group, 10.36.3

Style, 4.20.2

R-groups, 17.5.3

link, 18.1.40

REAL, 10.5.5, 13.5

Search, 3.6.2.12, 3.6.2.13, 3.6.2.14, 3.6.2.15, 3.6.2.16

RESP charges, 15

Field, 3.6.2.13

RIDE, 19.5

Homology, 3.6.2.15

RIDGE, 19.5

Identity, 3.6.2.14

- Rapid Docking GPU Engine, 13.5

Sequence, 3.6.2.16

RMSD, 5.5.2, 9.23.18

convert, 5.1.2

RMSF, 9.23.18

PFAM, 3.6.1.7

RNA, 4.17

PLOT.Yratio, 4.20.8

backbone conformation, 5.6.12

color, 4.20.8

chain analysis, 5.6.12

date, 4.20.8

conformation, 5.6.12

draw Tics, 4.20.8

pucker, 5.6.12

font, 4.20.8

structure analysis, 5.6.12

fontSize, 4.20.8

sugar conformation, 5.6.12

labelFont, 4.20.8

RTCNN, 12.1.9

lineWidth, 4.20.8

Score, 17.21

logo, 4.20.8

Ramachandran Plot, 5.6.9

markSize, 4.20.8

Real Format, 4.20.10

orientation, 4.20.8

Reinforce Helix Tool, 17.21

paper Size, 4.20.8

Relax Geometry Command, 17.21

previewer, 4.20.8

Label Shift, 4.20.7

rainbowStyle, 4.20.8

Style, 4.20.7

seriesLabels, 4.20.8

Residue Replacement, 17.21

PLS, 11.1

RotB, 23.8.7, 23.8.10

Rotational symmetry axis, 5.6.11

Water Radius, 4.20.10

SALI, 10.36.5, 22.6.11

Wilson, 10.36.2

SAR, 11, 16.6, 18.4.25, 18.6

Wire Style, 4.20.1

table, 10.36.3, 22.6.9

Working with the Hitlist, 12.4.1.2

SCARE, 12.6.4

XPDB Directory, 4.20.2

SCORE, 23.5.6, 23.5.17

Xstick, 3.7.1

SDF, 10, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 13.1.3, 18.2

a-bright, 3.7.2

SEQUENCE.site Colors, 4.20.4

about model, 11.1.3

SITE.label Style, 4.20.7

acceleration, 9.8.5

labelOffset, 4.20.7

acceptor, 10.4.9, 10.38.1

wrap Comment, 4.20.7

active, 7.7, 23.3.3

SLIDE.ignore Background Color, 4.20.4

activeICM, 7.8

Fog, 4.20.4

activeicm, 7.7, 7.12, 7.14, 7.14.1, 23.3

SMILES, 10.1.2, 10.2.4, 10.4.12

advanced, 7.14

Score, 12.1.9

background images, 7.15

Select Min Grad, 4.20.10

control, 7.13

Sequence Editing, 17.21

activeicmjs, 7.16

Show Res Code In Selection, 4.20.7

activity, 11, 18.6

Sidechain Optimization, 17.21

cliff, 10.36.5, 10.36.6, 22.6.11

Smiles, 23.8.7, 23.8.10, 23.8.11

tutorial, 22.6.11

South conformation, 5.6.12

add database, 10.10.3

Special Cases, 10.34.1.1

new data, 10.3.7

Structural alignment, 5.6.11

to table, 17.5.7

Subunits, 5.6.11

adding fragment, 10.4.8

SureChEMBL, 4.16.3

in editor, 10.4.8

Swissprot, 3.6.1.7

adjust row height, 23.2.39

Dat, 4.20.2

administration, 10.10.5

link, 18.1.40

advanced alignment selection, 8.7.14

Symmetry, 5.6.11

ai, 17.18

TYM, 9.13, 9.13.1

decoration, 17.18

TYR, 9.13, 9.13.1

alanine, 12.6.4

Temp Directory, 4.20.2

album, 6.15.3

Terminal Capping, 17.21

alias, 10.4.5

Tools Analysis, 5.6.12

align, 4.12, 10.14

Torsion Minimization, 17.21

color 2D scaffold, 10.14

Trimer, 5.6.11

dna protein, 8.6.4

USER.email, 4.20.11

multiple, 8.6.5

friends, 4.20.11

sequence structure, 8.6.3

full Name, 4.20.11

two sequences, 8.6.2

organization, 4.20.11

DNA to protein, 8.6.4

phone, 4.20.11

sequence, 8.6, 8.6.6

Ultra Large Libraries, 19.5

two sequences, 8.3.5, 8.6.2

Uniprot, 18.1.40

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, 22.4.4, 23.4.12, 23.6, 23.6.2

VHL, 12.14

annotation tutorial, 22.4.4

VLS, 13.1, 13.1.1, 13.1.2, 13.1.9.2

box shade font, 8.7.7

preferences, 13.1.4

editing, 8.7.1

Van Drie, 10.36.5

editor, 8.7

Label Style, 4.20.7

example, 8.3.14

Volume, 23.8.7, 23.8.10

font size, 23.2.1

Change, 13.1.9.4

format, 8.7.11

image, 8.7.2

store, 6.10.7.4

profile, 22.4.4

animations, 7

reorder, 8.3.12

annotate, 4.6.21, 10.13

search, 8.7.12

alignment, 8.7.6

secondary, 22.4.4

by substructure, 10.13

structure, 8.7.16, 23.6.2

plot, 18.4.24

selection, 8.7.13

annotation, 8.7.6

strength, 8.3.8

antialias, 3.6.1.15, 3.6.3.10

profile, 8.3.8

lines, 3.6.3.17

view options, 8.7.10

lines, 3.6.3.17

color, 8.7.9

apf, 5.5.6, 5.9, 10.37.5, 10.37.6, 10.38, 11, 12.7, 13, 13.1.9.5, 13.3, 13.4, 17.3.11, 17.17, 22.8, 22.8.1, 22.8.2, 22.8.3, 22.8.4, 22.8.5, 23.8.12

comment, 8.7.6

flexible template, 10.37.6

consensus, 8.7.9, 8.7.14

pairwise, 10.37.5

cut, 8.3.11

super, 10.37.3

display title, 8.7.10

template, 17.12.3

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, 22.8

options, 8.7.10

cluster, 22.8.5

rename, 8.7.10

consensus, 22.8.2

reorder, 8.3.12

score, 22.8.3

ruler, 8.7.10

screen, 22.8.4

save, 8.7.2

superposition, 22.8.1

search, 8.7.12

alignment, 10.37.7

selection, 8.7.13, 8.7.14

apf3Dqsa, 23.8.12

sequence offset, 8.7.10

apo, 13.1.10

table, 8.7.10

append, 18.1.44

view, 8.7.10

table, 18.1.44

alignments, 8.6, 22.4

rows, 3.6.10.7

allosteric, 5.7.7

applying prediction models, 11.2

alpha, 3.7.2

area, 5.6.3, 5.7.6, 12.13, 12.13.2, 12.13.3, 22.3.5

channel, 4.20.6

aromatic, 5.3, 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, 23.2.8

amidinium, 10.15

as2_graph, 4.6.5

amino acid, 4.17, 9.13

as_graph, 23.2.8

acids, 9.13.1, 10.4.6

asparagine, 9.23.2

anaglyph, 6.6, 23.1, 23.1.8

assign, 6.1.3

stereo faq, 23.1.8

2D coordinates, 10.20.2

analysis, 3.6.4, 8.3

helices, 5.7.1

charge states amino acids, 9.13

strands, 5.7.1

angle, 5.6.7, 5.6.8, 6.8.5, 6.9, 6.12.6, 10.16, 23.2.18, 23.4.16

atom, 4.20.5, 10.3.28, 23.2.4, 23.2.5, 23.2.8, 23.2.16, 23.2.17, 23.4.10

angstrom, 23.4.7

charge, 23.4.21

animate, 3.6.3.15, 6.10.7

atomLabelStyle, 4.20.7

view, 6.10.7

atomic energy circles, 17.3.5

animation, 6.10.7.1, 6.10.7.2, 6.10.7.3, 6.10.7.4

partial charges, 15

score, 10.38.2

bioinfo align multiple, 8.3.7

fields, 5.5.6, 5.9, 10.38, 10.38.1, 10.38.3, 13, 22.8

two sequences, 8.3.5

attachment, 10.4.3, 10.5.1

links, 8.3.9

point, 10.35.4

menu, 3.6.4

author, 4.2.4

secondary structure, 8.3.2

close tree, 10.28.5

translation, 8.3.3

play slide, 7.13

bioisoester, 10.9

autofit, 12.11

bioisostere, 10.9, 10.9.1, 10.9.2, 17.8

autosave, 23.2.33

biological, 5.4.3

available properties, 10.11.1

biomolecule, 3.6.5, 5.4.3, 22.3.8, 22.3.12

ave, 18.7.1

bit, 23.1.3

avi, 6.16, 6.16.2

blast, 4.16.4, 8.4

axes, 18.4.15

search, 4.16.4

axis, 18.4.11

blood brain barrier, 10.11.6

options, 18.4.10

blue lines, 8.2

grid, 18.4.10

boat, 23.5.20

range, 18.4.10

boltz, 4.3, 9.8, 9.8.1, 9.8.1.1, 9.8.2, 9.8.2.1, 9.8.3, 9.8.4, 9.8.5, 9.8.6, 9.8.6.1, 9.8.7

title, 18.4.10

co fold complex, 9.8.1

b-factor, 5.7.5, 9.8.3, 22.3.10

folding, 9.8

coloring scale, 23.2.38

confidence model, 9.8.3

backbone, 6.1.10, 23.2.13

conformations, 9.8.2

background, 6.4.2, 6.4.3

diffusion stack, 9.8.2.1

color shortcut, 23.2.2

multiple sequences, 9.8.1.1

images activeicm, 7.15

reference, 9.8.7

image, 6.4.3

run cpu, 9.8.5

backup, 3.6.2.11

weights update, 9.8.4

bad, 10.11

boltz2, 9.8, 9.8.7

groups, 10.4.9

bond, 5.1.3, 5.3.1, 5.3.1.1, 5.3.1.2, 9.11, 10.4.10, 23.4.1, 23.8.7, 23.8.10

ball, 4.20.5

covalent, 23.4.2

and stick, 3.7.1

type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3

balloon, 18.4.26

bonding, 6.1.8

bases, 10.4.6

preferences, 4.20.1

basicsel, 4.6.2

box, 4.20.7, 6.8.16, 8.7.7, 8.7.7.1, 23.5.9

set, 15

alignment, 22.4.4

batch, 12.3.2, 12.13.9

size, 17.9.1

file, 12.3.2.2

browse, 10.3.31, 20.4

index, 12.3.2.4

mode, 10.3.31

loaded icm object, 12.3.2.1

molt, 19.2

mol mol2, 12.3.2.3

stack, 9.23.15

molcart, 12.3.2.5

build, 6.10.7.1

run, 12.3.3

2D qsar, 11.1.2

bayesian classifier, 11

homology model, 9.1.2

bbb, 10.11.6

hydrogens, 9.23.5

beep, 23.2.35

buried molSurface, 13.1.9.4

begin docking simulation, 12.3

buttons, 7.14

best, 10.3.34

bye, 3.6.1.19

bicyclics, 10.4.6

alpha, 6.1.10

binding, 22.5.3, 23.2.14, 23.5.2, 23.5.10

trace, 6.1.10

pocket, 9.20

ca-trace, 6.1.10

properties, 6.3.1

cache, 7.14.1

properties, 10.11

fragments, 10.3.33

sequence similarity, 8.7.15

group, 10.4.5

startup, 23.10.2

groups, 10.4.5, 10.4.8

carbon, 23.2.4, 23.2.5

modifiers, 10.35.2

carboxylic acid, 10.15

properties, 22.6.4

cartesian, 10.23

right click, 10.4.3

cation, 5.3.2

search, 10.5, 13.4

cavities, 5.6

filter, 10.5.2

closed, 5.6.4

text, 10.5.4

ccp4, 23.2.27, 23.2.28

sketch, 22.6.1

cell, 5.4.2

space, 10.30

center, 3.6.3.20, 4.4, 6.12, 6.12.5, 17.3.13, 18.1.40, 23.4.22

spreadsheet, 4.16.2, 10.1.3, 10.3.1, 10.4.14, 22.6.1, 23.8.13

on ligand, 17.3.13

compare, 10.3.22

and representative members, 18.7.2

template, 10.3.2

cereblon, 12.14

spreadsheets, 10.3

chain.breaks, 23.2.34

substituent, 10.9

chair, 23.5.20

substructure, 4.2.2

change box size, 17.9.1

table, 17.10, 23.8.11

height of all rows, 18.1.7

display, 10.3.3

ligand, 17.5.1

tables, 18.2

residue number, 9.2

toxicity, 10.11.3

row height, 18.1.7

2D, 10.7

selection, 4.6.7

3D, 10.7

speed range, 6.10.7.2

append, 10.4.13

changing font in alignment editor, 8.7

clustering, 10.28, 10.28.1

charge, 3.6.3.21, 5.1.3, 5.1.3.1, 5.1.3.2, 6.8.2, 9.13.1, 10.4.3, 10.5.1, 10.7.1, 10.7.2, 10.7.3, 10.38.1, 13.1.9.4, 23.4.1

convert, 5.1.3, 5.1.3.1, 5.1.3.2, 9.23.1, 10.7, 10.7.1, 10.7.2, 10.7.3, 23.4.1

groups, 12.2.1.3, 23.5.22

display.fit, 23.8.13

states, 9.13, 9.13.1

draw, 10.4.1

check box, 7.6.6

duplicates, 10.3.21

convert, 23.8.5

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, 18.7.1, 22.6.4, 23.8.4, 23.8.5, 23.8.7, 23.8.8, 23.8.9, 23.8.10

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, 23.8.15

superposition, 10.37.3, 10.37.7

dictionary, 10.4.4, 10.4.5, 10.4.6

table, 10.3, 18.2

draw, 22.6.1

cheminformatics, 10, 10.3, 23.8

spreadsheet tutorial, 22.6.1

tutorials, 22.6

edit buttons, 10.4.11

chemistry, 10.24, 23.8

editor, 10.4, 10.4.8

convert, 10.20

not starting, 23.1.13

2dto3d, 10.20.1

fingerprint, 16

pca, 10.29

fingerprints, 23.8.15

smiles, 10.20.3

remove.redundant, 10.33

alignment, 8.8

chemlib.so, 23.1.3

chemical, 10.3.35

chemspace, 10.5.5

faq, 23.2.20

append, 22.6.4.4

key, 23.2.38

build visualize, 22.6.4.1

scale, 23.2.38

compare, 22.6.4.8

surface by proximity, 6.3.3

delete row, 22.6.4.3

selection, 6.3.4

distinguish, 22.6.4.7

table, 10.3.27

export, 22.6.4.5

2D sketch, 10.5.6.5

project, 22.6.4.6

background, 3.6.3.18, 6.4.2

select, 22.6.4.2

distance, 6.8.10

chi, 6.8.5, 23.2.18

mesh, 6.3.9.3

chimeric ligands, 12.9

table, 10.3.27

chiral, 10.25, 12.1.3

coloring, 6.4.1

chirality, 10.25, 12.1.3

column, 18, 18.1.6, 18.1.22, 18.1.25, 18.1.39, 18.1.40, 18.4, 18.4.1, 23.8.7

considerations, 12.1.3

annotation, 18.1.41

chrome, 23.3

order, 18.1.29

cis trans proline, 22.5.2

plot, 18.4.6

citation, 9.8.7

row width, 18.1.22

clash, 4.20.5, 6.8.15

statistics, 18.1.32

volumes, 13.1.11

visibility order, 18.1.28

classes, 10.3.28

color, 18.1.10

classification model, 16.5

hide, 10.3.8

clear display and planes, 3.6.3.2

show, 10.3.8

selection, 4.6.6

combinatorial chemistry, 10.35

planes, 3.6.3.2

library, 22.6.8

click, 4.13, 6.11, 6.12

combine, 3.6.10.5

clip, 6.3.10, 6.13.1, 23.2.11

display style, 4.20.9

clipboard, 6.15.3, 18.7.3

command, 23.5.16

clipping, 23.2.19

line, 23.2.32

planes, 6

commands, 23.10.1

tool, 6.13

common substructure, 10.37.1

tools, 6.13

compact tree, 10.28.5

clone, 3.6.1.2

compare, 10.3.29, 10.31, 10.32

close, 6.3.3, 6.3.4, 17.23

table, 10.3.22

downstream cluster, 10.28.5

tables, 10.31

project, 17.23

compatible, 3.6.1.10

cavities, 5.7.7

complex, 9.8.1, 10.6, 13.1.9.3

cloud, 13.1.7, 13.1.7.2

compound, 4.2.4, 10.24, 18.2

cluster, 9.23.18, 13.1.7, 13.1.9.5, 18.7.1

compounds, 23.9.3

stack, 9.23.18

compress, 4.20.6

representative.center, 10.28.2

compressed, 18.1.6

clustering, 18.7, 22.6.3

table view, 18.1.6

cns, 10.34

conditions, 10.5.2

co-folding, 9.8, 9.8.1, 9.8.1.1

gen, 10.23

collada, 3.7.6, 6.3.7

confidence model, 9.8.3

color, 5.7.4, 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, 18.1.45, 18.7.4, 23.2.4, 23.2.5, 23.2.16, 23.2.20

configuration error, 23.1.19

alignment, 8.7.9

conformation, 9.23.18, 10.23, 12.6.2

background, 6.4.2

conformational entropy, 10.27

by, 6.4

stack, 15

conformer energies, 15

crystal, 5.4.2

conformers, 10.23

crystallographic analysis, 5.4

connect, 6.3.9.1, 6.12, 6.12.7

biomolecule, 5.4.3

object, 6.12.7

contour map, 5.4.6

connectivity, 10.4.3, 10.5.1

convert2grid, 5.4.7

consensus, 10.38, 22.8.2

crystallographic cell, 5.4.2

pharmacophore, 10.38.1

load eds, 5.4.4

construct, 3.6.1.1, 6.10.7.1

maps cell, 5.4.5

molecule, 3.6.1.1

symmetry packing, 5.4.1

object, 3.6.1.1

tools, 22.3.8

contact, 5.6, 5.6.3, 22.3.5

cell, 3.6.5

surface, 6.3.2

neigbor, 5.4.1

contacts, 6.3.3, 6.3.4, 10.6, 13.1.9.6, 17.3.12

neighbors, 3.6.5

contour, 5.4.6, 5.4.7

crystallography, 5.4.4, 5.4.6, 5.4.7, 23.2.27, 23.2.28

convert, 5.1.2, 10.20.1, 10.20.5, 23.8.5

csv, 10.2.3, 18.1.2, 18.1.3, 18.1.21, 20.2

chemical, 10.3.24

current, 23.2.22

2D 3D, 10.7

slide, 7.13

3D molecular editor, 10.4.16

curves, 18.4.5

from pdb, 5.1.3

custom, 6.12, 10.3.3, 10.37

local database, 3.6.1.6

actions, 18.1.40

pdb, 5.1.2, 22.3.2

fragments, 10.13

chem, 10.7.1

label, 6.8.8

smiles to 2D, 23.8.11

rotation, 6.12.2

local.database, 3.6.1.6

customized MPO score, 10.34.1

smiles, 10.20, 10.20.3, 10.20.4

cut, 18.1.35

coordinates, 10.1.3

vertical alignment block, 8.3.11

copy, 10.3.25, 10.4.11, 10.4.18, 10.5.6.2, 18.1.35

cyclic peptide, 9.22

cell, 18.1.36

cys, 5.7.3

chemical, 10.3.25

cysteine reactivity, 5.7.3

loop, 9.5

damaged skin, 23.1.12

paste row, 18.1.35

dash, 23.2.12

row, 18.1.36

database, 8.4, 10.10, 10.35.4, 13.1.3, 13.1.6, 19.1, 20

rows, 18.1.44

file format, 13.1.3

selection to table, 18.1.37

search and alignment, 8.4

chemical, 10.3.16

databases, 23.9.3

corso, 9.8.7

novo, 12.10

covalent, 17.10.1

design, 12.9

bond, 5.7.3, 22.9.3

decompose.library, 22.6.9

docking, 12.8, 12.8.1, 17.16, 22.9.3

decomposition, 10.35.4, 10.36.1, 18.4.25

tutorial, 22.9.3

decoration, 17.18

cpk, 6.1.5, 23.2.21

default, 4.14

cpu, 9.8.5

delete, 3.6.2.1, 4.6.6, 7.6.8, 23.4.9

crash, 3.6.2.11

alignment, 8.7.5

creat, 7.6.1

all, 3.6.2.2

create, 18.1.1

column row, 18.1.38

markush, 10.35.3

label, 6.8.9

new objects, 4.17

alignment, 8.7.5

cross, 23.2.10

all, 3.6.2.2

section, 6.13

angle.label, 6.9.4

cryptic, 5.7.7

column, 18.1.38

label, 6.8.9

chemical, 10.3.3

row, 18.1.38

dihedral.angle, 6.9.3

selection, 3.6.2.1

distance, 6.8.10, 6.8.14, 6.9.1

tether, 9.23.5

electrostatic, 3.6.3.21

dendrogram, 10.30.1

energy.gradient, 6.8.17

denoising, 9.8.2.1

hydrogen, 6.1.7

denovo, 12.9

polar, 6.1.7

density, 5.4.4, 5.4.6, 5.4.7, 23.2.27, 23.2.28

macroshape, 6.3.6

functional theory, 15

meshes, 6.3.5

depth, 6.3.12, 6.10.5

and display.macroshape, 3.7.6

deselect, 23.2.7

molecule, 10.3.24

design loop, 9.4, 9.23.10

origin, 6.8.12

deviation, 23.4.7

potential, 3.6.3.21

dfa, 16.3.3

representations, 3.7.1

dfz, 16.3.2

restraints, 6.8.14

dialog, 7.6.5

ribbon, 6.1.3

diffuse, 3.7.2

skin, 6.1.4

diffusion, 9.8.2.1

status, 23.2.32

model, 9.8

surface, 6.1.6, 6.3.1

runs, 9.8.2

surfaces, 3.7.6

stack, 9.8.2.1

table, 10.3.3

dihedral, 5.6.8, 6.8.5, 23.2.18

tethers, 6.8.13

angle, 5.6

wire, 6.1.1

dimensional, 23.8.6

xstick, 6.1.2

directories preferences, 4.20.2

distance, 5.6, 5.6.6, 6.8.10, 6.9, 10.31, 23.2.12, 23.4.8, 23.4.10

directory, 4.20

faq, 23.4.10

disappearing labels, 23.1.12

restraint, 12.5

dislay ligand receptor interaction, 10.6

label, 4.20.7

display, 4.5, 4.14.1, 4.20, 5.3, 5.3.1, 5.3.1.1, 5.3.1.2, 6.8.15, 6.14, 10.25, 12.2.1.3.3, 23.2.4, 23.2.5, 23.2.8, 23.2.10, 23.2.11, 23.2.17, 23.2.21, 23.2.30, 23.2.32, 23.4.10, 23.4.11, 23.4.20, 23.8.4

distances, 3.7.3

chemical, 6.8.11

disulfide, 9.11, 9.18

delete distances, 6.9.4

bonds, 9.18

dihedral, 6.9.3

diverse set, 18.7

distance restraints, 6.8.14

dock, 12, 12.11, 17.10, 17.10.1, 22.9.3, 22.11.1, 22.11.2, 22.12.1, 23.5.3, 23.5.4, 23.5.5, 23.5.7, 23.5.8, 23.5.10, 23.5.11, 23.5.12, 23.5.13, 23.5.14, 23.5.15, 23.5.16, 23.5.21

distance2, 6.9.1

apf, 17.17

angles, 6.9

chemical table, 12.3.4

formal charge, 6.1.9

command, 23.5.16

gradient, 6.8.17

macrocylce, 23.5.20

hbond, 13.1.9.3

start, 12.1

hbonds, 13.1.9.4, 17.3.4

table, 17.10

hydrogen, 6.1.7

covalent, 17.10.1

atoms ligand editor, 17.3.3

docked ligand strain, 12.1.10

mesh, 6.3.5

docking, 5.7.6, 9.8.6, 12, 12.1, 12.2, 12.2.1, 12.4.1.4, 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, 17.10, 17.10.1, 17.11, 22.9, 22.9.1, 22.9.2, 22.11.3, 22.12, 22.12.2, 23.5, 23.5.1, 23.5.9, 23.5.17, 23.5.18

meshes, 6.3.8

batch index, 12.3.2.4

options, 17.3

covalent, 12.8

planar angle, 6.9.2

display, 12.4.1.5

tab, 3.7.1, 23.2.16

explicit group, 22.12.2

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

display, 12.2.1.3.3

easy rotate, 3.6.3.12

general, 12.2.1.3.1

ecfp, 11.3

project, 9.8.6.1, 13.1.5

edit, 5.3.1.1, 17.5.8, 23.8.3

table, 13.1.5

2D, 17.5.1

results display, 12.4.1.5

add sequence, 10.4.17

setup, 23.5.13

alignment, 8.7.1

start, 12.2.1

chemical moledit, 10.3.26

steps, 12.2

ligand, 17.5, 17.5.1

template, 12.7

2D, 17.5.1

templates, 17.12.3

editor preferences, 17.2

tutorials, 22.9

multiple substituents, 17.5.2

waters, 12.1.8

tools, 3.6.2.17

background, 23.5.19

menu, 3.6.2

batch, 12.3.2

molecular document, 7.6.1

conformations, 23.5.20

molecule, 10.4

flexible.rings, 23.5.20

molt, 19.3

interactive, 12.3.1

selection, 3.6.2.5

preparation, 12.2.1

slide, 7.4.1

procedure, 12.3

table row, 18.1.24

results, 12.4

molecule, 10.3.26

sampling, 23.5.20

structure, 10.3.26

template, 12.7

editor, 23.4.12

document, 7.6.4, 7.6.5

editpdbsearch, 3.6.2.12

navigation, 7.6.7

eds, 5.4.4, 5.4.6, 5.4.7

documents, 6.15.3

effect of mutation, 9.16, 9.17

dollar, 23.10.3

on binding tutorial, 22.5.3

donator, 10.4.9

example2, 22.5.3.1

envelope, 3.7.1

stability tutorial, 22.5.4

surface, 4.20.5

effort, 10.23, 10.37, 23.5.12

dotted line, 6.1.3

electron, 5.4.4, 5.4.6, 5.4.7, 23.2.27, 23.2.28

lines, 23.2.34

denisty map, 5.4.5

double, 10.4.10

density map, 3.6.1.7, 3.6.5, 5.4.4, 5.4.6, 12.11

doublet, 10.4.7

contour, 3.6.5

download, 23.1.1, 23.9.3

electrostatic coloring scale, 23.2.38

weights, 9.8.4

potential, 3.6.3.21, 15

dpc, 16.3.4

surface, 6.3

drag, 4.12, 4.20.7, 6.8.3, 7.6.4, 8.6.6, 23.4.5

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, 20.7

draw, 10.4.18, 10.35.5, 23.8.2

embed browser, 7.11

chemical, 10.4.1

powerpoint03, 7.8

drop, 4.12, 7.6.4, 8.6.6, 23.4.5

powerpoint07, 7.9

drug, 10.11, 23.8.7, 23.8.9

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

empty hostid, 23.1.18

path, 23.3.3

enamine, 10.5.5

alignment secondary structure, 23.6.2

real, 13.5

apf model, 23.8.12

enantiomer, 23.5.21

atom charge, 23.4.21

enantiomers, 12.1.3

display, 23.2.17

endocyclic torsion angles, 5.6.12

autosave, 23.2.33

energy, 5.7.4, 6.8.15, 10.27, 10.27.2, 23.5.1, 23.5.2, 23.9.8

backbone, 23.2.13

circles, 13.1.11

background color, 23.2.2

maps, 12.2.1.1, 12.2.1.2

job, 23.5.19

minimization, 15

beep, 23.2.35

terms, 9.23.19

binding energy, 23.5.2

ensemble, 12.6.2

blend transition, 23.2.31

calculations, 9.23.18

breaks, 23.2.34

entropy, 10.17, 10.27.1

change torsion, 23.4.16

enumerate formal charge states, 10.18

chem table display, 23.8.4

reaction, 22.6.10

chemical monitor, 23.8.10

enumeration, 10.35.4

query2, 23.8.1

eps, 10.2.6

cheminformatics, 23.8

epsilon, 23.4.15

clipping plane, 23.2.11

eraser, 10.4.11

closest, 23.4.22

errno, 23.1.3

color carbon, 23.2.4

error, 23.1.3, 23.1.19, 23.2.35

skin, 23.2.16

evaluate score strain, 17.4

command line display, 23.2.32

exact, 10.31

convert chemical from pdb, 23.4.1

excel, 10.2.3

covalent bond, 23.4.2

exclude fragment, 10.5.2

delete, 23.4.9

volume, 17.3.11

descriptors, 23.8.15

exit, 3.6.1.19

deselect, 23.2.7

point, 17.19

dihedral, 23.2.18

explicit, 10.3.28, 12.6.1

dock charge groups, 23.5.22

flex, 12.6.1

probe, 23.5.13

group, 12.6.3

racemic, 23.5.21

docking, 12.6.3

repeat, 23.5.5

groups, 22.12.2

working directory, 23.5.23

export, 5.6.10, 20.4

docking, 23.5

dock project, 17.22

docktime, 23.5.11

pdb, 4.19

dollar, 23.10.3

extra windows, 6.2

download install, 23.1.1

extract, 4.18.2, 8.1, 10.1.3, 23.4.12, 23.8.8

druglikeness, 23.8.9

2D, 10.1.1

energy, 23.5.1

3d coordinates to spreadsheet, 10.1.3

error admin, 23.1.10

icb, 3.6.1.5

extract ligand, 23.8.8

object icb, 4.18.2

flexible dock, 23.5.15

sub alignment, 8.3.10

ring docking, 23.5.20

icb, 3.6.1.5

font size, 23.2.1

pharmacophore, 10.5.6.4

foreground table, 23.10.4

faq, 23, 23.2, 23.2.13, 23.4, 23.5, 23.7, 23.10, 23.10.2

gl failure, 23.1.11

ISISdraw, 23.8.3

gui, 23.2

MolCart, 23.9

guided dock, 23.5.3

activeicm, 23.3

hitlist, 23.5.7

iSee, 23.2.30

transparent ribbon, 23.2.3

icmPocketFinder, 23.5.10

truncate mesh, 23.2.15

insert column, 23.8.7

view stack, 23.9.8

installation, 23.1

weak hydrogen bonds, 23.4.20

interactions, 23.2.12

write pdb, 23.4.3

ligandbox, 23.5.9

faqcontour, 23.2.28

measure distance ring, 23.8.16

faqhbondstrength, 23.2.29

merge, 23.4.5

faqmaps, 23.2.27

modeling, 23.7

faqoda, 23.2.26

molcart 64bit, 23.1.3

faqstereo, 23.1.14

query, 23.9.5

fasta, 8.1.5

sdf, 23.9.4

fbdd, 13.2

text search, 23.9.6

fft, 12.13.1

molecule c, 23.2.5

protein protein docking, 12.13.1

moledit, 23.8.2

file, 3.6.1.3

movie planes, 23.2.19

close, 3.6.1.13

newscript, 23.10.1

compatible, 3.6.1.10

nmr, 23.4.18

export, 3.6.1.12

nvidia error, 23.1.2

high quality image, 6.15.1

origin, 23.2.10

load, 3.6.1.7

plist, 23.1.9

menu, 3.6.1

pmf score, 23.5.6

password, 3.6.1.11

pockets, 23.2.14

preferences, 3.6.1.16

preserve coordinates, 23.8.6

quick image, 3.6.1.14

quad buffer, 23.1.7

icb, 4.11

receptor selection, 23.5.14

recent, 3.6.1.17

reload dock, 23.5.4

bak, 3.6.2.11

remove salt, 23.8.14

filter, 19.2, 23.2.4

select, 23.2.6

selection, 4.6.8

renumber, 23.4.4

filters, 13.1.5

residue number selection, 23.2.36

find chemical, 10.3.32

rmsd, 23.4.7

fingerprint, 11, 11.3, 22.13, 23.8.1, 23.9.5

rmsdtips, 23.4.8

method, 11.3

rocking active ppt, 23.3.1

fingerprints, 23.8.15

speed, 23.3.2

firefox, 23.3

rotate chemical, 23.8.13

fit, 10.3.34, 12.11, 23.5.15

scale display, 23.2.38

fitting, 12.11, 18.4.16

scanScoreExternal, 23.5.17

five-membered ring conformation, 5.6.12

scanScoreExternal2, 23.5.18

fixed torsion, 15

score, 23.5.8

flexibility, 5.7.5, 12.6.3, 22.12

script, 23.10

flexible, 10.37, 12.6, 12.6.1, 12.6.2, 22.12.1, 23.5.15

sequence secondary structure, 23.6.1

APF superposition to template, 10.37.4

alignments, 23.6

docking, 17.13

smiles, 23.8.11

receptor, 9.8.6

solvent accessible surface table, 23.4.19

groups, 17.13

ss, 23.4.17

ring sampling level, 12.2.1.3

structure, 23.4

flood, 9.23.17

superimpose, 23.4.6

fog, 3.6.3.5, 6, 6.10.1

surface display, 23.2.37

font, 4.20, 4.20.7, 5.3.1.1, 6.8.2, 6.8.3, 8.7.7, 8.7.7.1, 10.3.28, 18.1.40, 18.7.4

thoroughness, 23.5.12

preferences, 4.20.7

force weights update, 9.8.4

display, 5.1.3.1, 5.1.3.2, 10.7.2, 10.7.3

view, 18.1.5

tutorial, 22.1

formal, 5.1.3, 23.4.21

2D3D labels, 22.1.4

charge, 6.1.9, 10.15, 10.18

annotation, 22.1.2

format, 18.1.2, 18.1.40

color representation, 22.1.1

formula, 10.4.9, 10.11

labels, 22.1.3

fragment, 10.3.35, 10.36.1, 13, 13.2, 17.11

user interface, 23.2

linking, 17.11

graphics, 5.3, 5.3.1

screening, 13.2

card, 23.1.2

fragments, 10.8

controls, 6

frame, 8.3.3

defects, 23.1.12

free energy, 9.14, 9.15

effects, 6.10

radical, 10.4.7

panel, 6.2

wilson regression analysis, 10.36.2

preferences, 4.20.3

freedomspace, 10.5.5

shadow, 3.6.3.13, 6.10.2

freeze column, 18.1.30

green arrows, 8.7.16, 23.6.2

row, 18.1.31

lines, 8.2, 23.6.1

frequency, 10.3.35

grid, 10.3.3, 10.37, 22.12.1, 23.8.4

front, 6.3.10, 6.13.1

grob, 4.20.5, 5.4.4, 5.4.6, 5.4.7, 6.3

full model, 9.1.3

group, 10.36.1, 17.6

builder, 9.1.3

column, 18.1.46

multiple chain, 9.1.3.1

groupGen, 17.18

refinement, 9.1.3

groups, 10.8, 10.11, 10.12

scene antialias, 3.6.3.10

guanidinium, 10.15

screen, 3.6.3.8

gui, 4.1, 4.20.4

function, 18.1.26, 18.1.32

menus, 3.6

functional, 15

preferences, 4.20.4

groups, 10.13

tabs, 3.7

furanose ring conformation, 5.6.12

guided docking, 12.5, 23.5.3

fuzzy, 12.7

h-bond, 5.3, 5.3.1, 5.3.1.1, 5.3.1.2, 23.2.12

gap, 9.4

halogen, 10.11.2

general preferences, 4.20.5

hardware, 9.8.5

generalselecttools, 4.6.1

stereo, 3.6.3.7, 23.1

generator, 5.4.3, 10.23

hba, 13.1.10

geometry optimization, 15

hbd, 13.1.10

getting started, 4

hbond, 5.2, 5.3, 5.3.1, 22.3.6, 23.2.29

giga search, 10.5.5

strength, 23.2.29

sized library, 13.5

header, 4.2.7, 18.4.9

gigasearch, 10.5.5

health, 5.7.4

ginger, 10.23

heatmap, 18.4.7

glasses, 6.6, 23.1.6, 23.1.14

example, 18.4.7.1

global side-chain sampling, 9.20

helix, 23.2.20

glutamine proline, 9.23.2

help, 2

google, 3.6.1.7

videos, 2

objects, 6.3.7

hetero, 10.3.28

3D, 3.7.6, 6.3.7

scan, 17.7

gpcr_model, 22.5.1

hidden block format, 8.7.11

gpu, 9.8.5

width, 8.7.11

graft loop, 9.5

hide, 18.1.39

graphical, 23.2.4

column, 18.1.28

quality, 3.6.3.11

activeicm, 3.3

highlight new data, 10.3.7.1

create molecular documents, 3.3.3

his, 23.4.15

slides, 3.3.2

histidine, 9.23.2, 23.4.15

getting started, 3.3.1

tautomer, 23.4.15

ppt, 3.3.4

histogram, 13.1.9.2, 18.4, 18.4.1, 18.4.9, 18.4.11, 18.4.13, 18.4.14, 18.4.15, 18.4.16, 18.4.17, 18.4.18, 18.4.20, 18.4.22

web, 3.3.5

bins, 18.4.3

chemical clusering, 10.28.1

options, 18.4.2

icm browser convert display pocket, 3.1.4

bin.size, 18.4.2

distances angles, 3.1.9

bins, 18.4.3

get started, 3.1.1

color, 18.4.2

graphical display, 3.1.2

source, 18.4.2

effects, 3.1.5

style, 18.4.2

images, 3.1.7

title, 18.4.2

labels annotation, 3.1.6

historeceptomics, 4.16.9

pro crystallographic tools, 3.2.6

hitlist, 12.4, 12.4.1, 13.1.8, 13.1.9.1, 13.1.9.5, 14.4, 23.5.7

get started, 3.2.1

cluster apf, 13.1.9.5

graphics, 3.2.2

export, 12.4.1.3

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, 9.9, 22.5

sequence analysis, 3.2.7

model, 9.1, 9.1.1.2

structure analysis, 3.2.3

introduction, 9.1.1

superimpose, 3.2.5

older versions, 9.1.1.3

surfaces, 3.2.4

hover, 18.4.26

selections, 3.1.3

3D editor, 22.7

superimpose, 3.1.8

add columns, 10.3.4

search, 4.16

cluster center, 10.28.2

hrydrogen.bond, 23.2.29

color 2D by ph4, 10.5.6.5

html, 3.6.1.12, 4.17, 7.6.1, 7.6.7, 23.3

copy 2D, 10.3.16

html-doc font size, 23.2.1

paste, 10.3.6

hybridization, 10.4.3, 10.5.1

decompose, 22.6.9

hydrogen, 5.3.1, 5.3.1.1, 5.3.1.2, 6.1.8, 10.4.3, 10.5.1, 22.3.6, 23.2.12, 23.8.7, 23.8.10

duplicate chemicals, 10.3.21

atom display, 17.3.3

edit table, 10.3.17

bond, 5.2, 6.1.8, 10.6, 13.1.9.3, 22.3.6

tree, 10.28.4

acceptors, 23.8.17

excel, 10.3.10

donor, 10.38.1

extract 3D ph4, 10.5.6.4

label edit, 5.3.1.1

filter, 10.3.12

move, 5.3.1.2

find replace, 10.3.13

bonds, 5.2.1, 12.1.5

mark row, 10.3.14

hydrogen-bond, 5.3, 5.3.1

markush, 22.6.8

bond, 10.4.9, 23.4.20

structure, 22.6.7

hydrogens, 10.3.28

merge tables, 10.3.23

remove, 10.3.18

properties, 10.3.19

hyperlink, 7.6.1, 7.6.2, 18.1.40

reactions, 22.6.10

hyrophobic, 10.38.1

reorder, 10.28.3

iSee, 3.6.1.5, 3.6.1.12, 4.11, 6.15.3, 22.2, 23.2.30, 23.2.31, 23.3.3

sdf, 10.3.9

icb, 4.18.2, 4.19, 9.8.6.1, 23.2.30, 23.3.3

show hide, 10.3.8

icm, 23.3.3

sort column, 10.3.5

chemist howto chemical search, 3.4.3

standardize, 10.3.18

cluster, 3.4.5

table hyperlinks, 10.3.15

combi library, 3.4.7

print, 10.3.11

ph4, 3.4.4

sketch, 3.4.1

restraint, 12.5

spreadsheets, 3.4.2

restraints, 12.5

stereoisomers tautomers, 3.4.6

interaction-strength, 5.3.1

pro 3D ligand editor, 3.5.1

interactions, 17.3.12, 23.5.2

chem3D, 3.5.2

interactive, 12.3.1, 22.2

chemsuper, 3.5.4

loaded ligand, 12.3.1.2

energy, 3.5.3

loop, 9.1.4.2

qsar, 3.5.5

modeling, 9.1.4

tutorials, 3.5

table ligand, 12.3.1.1

tutorials, 3.4

modeling, 9.1.4

hanging, 23.1.13

interface prediction, 22.10

object, 5.1, 22.3.2

internal hydrogen bonds, 12.1.5

script, 18.1.40

internet explorer, 23.3

icm-crash, 23.1.13

interrupt, 6.10.7.3

icmFastAlignment, 8.4

animation, 6.10.7.3

icmPocketFinder, 5.7.7, 23.2.14, 23.5.10

introduction, 1

icmdb, 20

invert selection, 18.1.23

icmjs, 7.16

invisible residue label, 23.1.12

icmpocketfinder, 22.3.7

ionization, 9.13, 9.13.1

id, 18.1.27

iqr, 18.4.23

identity, 4.2.3

isee, 7.6.5

image, 4.15, 4.20, 4.20.5, 6.15.3, 7.6.3, 10.2, 10.2.6, 18.4.21, 23.1.20

isis, 10.4.18

advanced, 6.15.3

isostere, 13.4

distortion, 23.1.20

isotope, 10.4.3, 10.5.1

preferences, 4.20.6

iupac, 10.2.7, 10.3.20

problem, 23.1.20

javascript, 7.16

multiple, 3.6.1.7

job, 23.5.19

quality, 3.6.3.11

join, 10.32

quick, 3.6.1.14, 6.15.2

jpg, 6.15

images, 6.15

means, 18.7.1

impose, 12.6.2

kcc, 16.3.1, 16.5

in-a-window, 23.1.7

keep carboxyls neutral, 12.2.1.3

inchi, 10.20.3

kernel regression, 16.3.1

increment, 18.1.27

chemical, 10.4.10

id, 18.1.27

keyboard mouse, 6.11

index, 23.9.6

keystokes in chem-edit, 10.4.10

induced, 23.5.15

kmz, 3.7.6, 6.3.7

fit, 9.8.6, 12.6, 12.6.1, 12.6.3, 17.13, 22.12, 22.12.1

knime, 21

insert, 7.6.4

label, 4.20.7, 5.3.1, 18.7.4, 23.2.17

column, 18.1.26

atoms, 6.8.2

image, 7.6.3, 18.1.34

color, 6.8.7

table, 18.1.34

move, 6.8.4

row, 18.1.33

residues, 6.8.3

script, 7.6.4

sites, 6.8.6

install, 1, 10.10.1, 20.1, 23.1.3, 23.1.4

variables, 6.8.5

installation, 23.1

2D, 3.7.3

interaction, 5.3, 5.3.1, 5.6.3, 10.6, 23.2.12

3D, 3.7.3, 6.8.1

fingerprint, 13.1.9.6

atom, 6.8.1

fingerprints, 13.1.9.6

atoms, 6.8.2

lists, 13.1.10

color, 6.8.7

delete, 6.8.1, 6.8.9

surface, 17.3.2

distance, 6.8.10

receptor contacts, 17.3.12

drag, 3.6.3.16

display, 5.2

move, 3.6.3.16, 6.8.4

interaction, 10.6

residue, 6.8.1

strain, 17.3.10

residues, 6.8.3

surface, 5.2.3

site, 6.8.1

tether, 17.12

sites, 6.8.6

vicinity, 9.20

variable, 6.8.1

ligand-based, 13, 13.3

variables, 6.8.5, 23.2.18

ligand-induced RNA conformational changes, 5.6.12

labeling, 6.8.1

convert, 9.23.1

labels, 6.8, 10.3.28

editor, 17, 17.1

distances, 6.8.10

binding.re-dock ligand, 17.9

tab, 3.7.3

display, 17.3

landscape, 4.20.6

edit, 17.5

large chemical space, 22.6.4

energy, 17.3

font, 23.1.16

hydrogen.bond, 17.3

size, 23.1.9

pocket, 17.3

sdf, 10.1.2

preferences, 17.2

layer, 6.14

restraint, 17.12

layers, 6.14

surface, 17.3

lbd, 9.8.6

tether, 17.12

command, 9.8.6.1

optimization, 22.11.3

docking, 9.8.6

pocket, 4.9

learn, 10.21, 10.22, 11, 11.1, 18.6, 23.8.12

receptor.contact, 5.6.3

learning, 11

ligand_pocket_interactions, 5.2.1

theory, 11.5

ligedit distance restraint, 17.12.2

least.squares, 18.4.16

tab, 3.7.5

library, 10.35.4

tether, 17.12.1

reaction, 22.6.10

light, 3.7.2

license, 23.1.4

tab, 3.7.2

ligand, 5.2.3, 5.3, 5.3.1, 9.8, 9.8.1, 10.6, 10.27, 10.27.1, 10.27.2, 12.1, 12.6, 12.13.6, 12.13.7, 17.3.12, 17.3.13, 17.5.8, 17.10, 17.11, 23.4.5, 23.4.11, 23.5.2, 23.5.9, 23.8.8

lighting, 6.3.9.4, 6.5

aide, 12.10

likeness, 10.11, 23.8.9

based screen, 10.38.3, 13.3

line, 4.20.5, 18.7.4, 23.2.12

best replace, 17.6

lineWidth, 4.20.3

binding, 9.17

link, 8.3.9

code, 4.2.4, 4.16.6

structure to alignment, 22.4

confidence, 9.8.3

linker, 12.14

considerations, 12.1.2

links, 4.6.20

editor, 17, 17.10, 17.10.1, 17.16, 17.17

linux, 10.10.1

bioisostere, 17.8

lipinski rule, 10.34

covalent docking, 17.16

list, 4.6.18

mrc, 17.15

liver, 10.11.5

preferences, 3.6.2.18

lmhostid, 23.1.18

energetics, 10.27

load, 3.6.1.3, 3.6.1.17, 5.4.4, 5.4.6, 5.4.7, 8.1

conformational entropy, 10.27.1

example alignment, 8.3.14

strain, 10.27.2

nmr model, 4.2.5

environment, 9.20

pdb hyperlinks, 4.2.6

optimization, 9.20

protein structure, 5.1.1

pocket, 5.2.1, 23.4.11

sequence, 8.1

from file, 8.1.4

selection, 4.6

paste, 8.1.2

level, 4.6.3

swissprot, 8.1.1

bond, 23.4.2

libraries, 9.23.6

disulfide, 9.11, 23.4.17

local, 23.2.24, 23.2.25

molecule, 3.6.1.1

boltz diffusion, 9.8.6, 9.8.6.1

object, 3.6.1.1

command, 9.8.6.1

making molecular slides, 7.1

databases, 19

html, 7.6

diffusion, 9.8.6

manual change torsion, 17.5.4

minimization, 9.20

map, 4.20.7, 5.4.4, 5.4.6, 5.4.7

database.browse, 19.2

cel, 5.4.5

edit, 19.3

maps, 12.2.1.1, 12.2.1.2, 12.13.8, 22.12.1, 23.2.27, 23.2.28, 23.5.9

query, 19.4

mark, 18.1.45

row, 19.3

row, 18.1.45

localpdb, 23.2.24

color, 18.4.14

localseq, 23.2.25

shape, 18.4.13

lock, 6.3.10, 6.13.1, 10.3.31

size, 18.4.13

log, 18.4.6, 18.4.11

markush, 10.28.7, 10.35.1, 10.35.3, 10.36.1, 22.11.3

logD, 10.11.8

docking, 22.11.3

logP, 10.4.9, 10.11

library, 22.6.8

logS, 10.4.9, 10.11

mass, 23.4.22

logarithmic, 18.4.11

matched pair, 10.36.6, 22.6.11

logout, 3.6.1.19

analysis, 10.36.6

loop, 9.3, 9.5, 23.2.20

materials, 3.7.6

analysis, 9.7

max, 18.7.1

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, 22.5.2

dendrogram, 10.30.1

tutorial, 22.5.2

mcs, 10.28.6, 10.30.1

modeling, 9.1.4.2, 9.6, 9.7, 9.23.10

rgroup decomposition, 10.28.7

preferred residues, 9.6

mean, 18.4.6, 18.4.23, 23.4.7

model, 9.23.9

measure distance, 23.8.16

sample, 9.23.9

to ring, 23.8.16

energy water, 9.23.17

median, 18.4.6, 18.4.23

mac, 10.10.1, 23.1.9, 23.1.16

membrane, 12.1.7, 14.3

font, 23.1.16

exposed docking, 12.1.7

size, 23.1.16

memory, 10.1.2

machine learning, 22.13

menu, 7.6.5

macrocycles, 9.22

chemistry, 3.6.14

macros, 7.14

docking, 3.6.15

macroshape, 3.6.3.22, 6.3, 6.3.6

homology, 3.6.13

make, 6.10.7.1, 18.1.1

molmechanics, 3.6.16

alignment, 8.6.1

tools chemical search, 3.6.11

animation, 6.10.7.1

molecular editor, 3.6.12

apf docking sar model, 16.6

windows, 3.6.17

complex, 13.1.9.4, 17.23

merge, 10.32, 23.4.5

flat, 23.8.13

two sets, 10.32

molecular document, 7.6

mesh, 5.2.2, 5.2.3, 5.4.4, 5.4.6, 5.4.7, 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

molt, 19.1

clip, 6.3.10

receptor maps, 12.2.1.2

color lighting, 6.3.9.4

representation, 6.3.9.3

documents, 22.2

save, 6.3.11

dynamics, 14, 14.1, 14.2, 14.3, 14.4

options, 6.3.9

membrane, 14.3

meshes, 6.3.2, 6.10.5

restraints, 14.2

surfaces grobs, 6.3

run, 14.1

tab, 3.7.6

vls, 14.4

metabolic oxidation, 16.7

editor, 23.8.2

min, 18.7.1

graphics, 6

minimization, 9.19

interaction display, 5.3

cartesian, 9.23.8

matched pairs, 22.6.11

global, 9.23.8

mechanics, 9.23

local, 9.23.8

convert, 9.23.1

minimum specifications, 1

design loop, 9.23.10

mmff, 9.23.6, 10.4.16, 23.2.17, 23.8.5

edit structure, 9.23.5

type, 6.8.2

gamess, 9.23.16

mmp, 22.6.11

generate normal mode stack, 9.23.14

mnSolutions, 4.20.10

his asn, 9.23.2

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, 9.9, 9.19, 22.5

ic table, 9.23.13

domain interaction, 9.19

impose conformation, 9.23.4

start, 9.1.1.2

minimize, 9.23.8

weight, 11.1.4

mmff, 9.23.6

weights, 9.8.4

regularization, 9.23.3

modelers view, 9.1.4.1

sample loop, 9.23.9

view, 9.1.4.1

peptide, 9.23.12

modeling, 9.23.3

protein, 9.23.11

options, 9.1.1.1

terms, 9.23.19

modeller view, 9.1.4

view stack, 9.23.15

models, 9.8.2

modeling, 9, 9.20, 15

modification history, 17.5.6

table, 10.20.2

modify, 9.13.2

weight, 10.4.9

amino acid, 9.13

molecule, 23.2.8, 23.8.3

group, 9.12

editor, 10.4

mol, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13, 22.11.2

moledit, 10.4.8

mol2, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6

molmechanics, 23.9.8

molcart, 10.10, 10.10.1, 10.10.2, 10.10.3, 10.10.4, 10.10.5, 19, 20, 23.1.3, 23.8, 23.8.1, 23.9.3, 23.9.4, 23.9.5, 23.9.6

minimize, 9.23.8

add database, 10.10.3

mmff, 9.23.6

administration, 10.10.5

molscreen, 13, 16

connect, 23.9.2

custom model panel, 16.4

download dbs, 23.9.3

load models, 16.1.1

hostid, 23.9.1

run, 16.1

installation, 10.10.1

model type, 16.3

license, 23.1.4

results, 16.2

search, 10.10.4

molskin, 6.3.2

start, 10.10.2

molsynth, 10.11.7

connect, 23.9.2

molt, 19, 19.4

hostid, 23.9.1

monitor, 23.8.10

license, 23.9.1

monochrome, 10.3.28

molclart, 23.1.4

montecarlo, 23.9.7

molecular, 5.3, 5.3.1, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.23, 23.8.7, 23.8.10

mouse, 4.4, 6.11, 6.12

animations slides, 7

mov, 6.16, 6.16.2

column, 18.1.28

zero, 9.8.2.1

mesh, 6.3.9.2

navigate workspace, 4.6.10

slide, 7.4.2

nconf, 9.8.2, 9.8.6.1

structure, 6.12

zero, 9.8.2.1

tools, 6

nearest, 23.4.22

rotate, 6.11

neighbors, 5.3.1

slab, 6.11

nephrotox, 10.11.4

translate, 6.11

neural network, 17.18

z-rotation, 6.11

Torsion Profile Neural Network Prediction Engine, 6.12.6.1

zoom, 6.11

new, 8.1

movie, 6.16.1, 23.2.19, 23.9.7

icm session, 3.6.1.2

montecarlo, 23.9.7

table, 18.1.1

making, 6.16, 6.16.2

table, 18.1.1

open, 6.16, 6.16.2

nmr, 23.4.18

mpa, 22.6.11

model, 4.2.5

mpeg, 6.16, 6.16.1, 6.16.2

nnc, 16.3.5

mpg, 6.16, 6.16.2

nntorsion, 6.12.6.1

mpo, 10.34

nof, 10.11.2

binary classification, 10.34.2

chemical, 10.11.2

custom step function, 10.34.1.2

non-contiguous selection, 4.6.18

customized, 10.34.1

non-covalent, 5.3

save, 10.34.1.3

normal modes, 9.23.14

special cases, 10.34.1.1

nucleic acid conformation analysis, 5.6.12

mtl, 6.7

geometry, 5.6.12

multi apf super, 10.37.7

nucleotide analysis, 5.6.12

panel, 6.2

conformation, 5.6.12

parameter optimization, 10.34

geometry, 5.6.12

template, 9.1.4.3

puckering, 5.6.12

windows, 6.2

number of sp3, 10.11.2

multimer, 9.8.1, 9.8.1.1

numbers, 10.3.28

multiple, 12.6.2, 22.12.1

nvidia, 23.1.2

chain, 9.1.2.2, 9.1.3.1

obj, 6.7

chains, 9.8.1.1

object, 4.12, 4.19, 22.3, 23.2.8

position group scan, 17.7

objects, 5.1.2

rec, 12.6.2

in table, 18.3

receptor, 4.16.1, 22.12

in.table, 18.3

docking, 17.15

occlusion, 6.3.12, 6.10.5

sequences, 9.8.1.1

shading, 6.3.12

protein, 23.2.5

effect, 6.10.5

mutant, 9.12, 23.4.13, 23.4.14

occupancy, 6.1.3, 22.3.10

mutate, 9.14, 9.15, 23.4.15

oda, 5.7.6, 12.13, 12.13.2, 12.13.3

residue, 23.4.13

older version, 3.6.1.10

N C, 23.4.14

omega, 6.8.5, 23.2.18

mutation, 9.12, 9.14, 9.15, 9.17, 22.5.3, 22.5.4, 23.4.13, 23.4.14

online databases, 10.5.5

protein binding, 9.14

open, 3.6.1.3, 4.18, 18.1.2

ligand, 9.17

file, 4.18

peptide, 9.16

password, 4.18.1

stability, 9.15

with password, 3.6.1.4

mysql, 20

movie, 6.16, 6.16.2

conformations, 9.8.2

password, 3.6.1.4, 4.18.1

optimize, 9.23.2

clone, 10.5.6.2

oracle, 20

draw2D, 10.5.6.1

orange, 4.6.5

draw3D, 10.5.6.2

selection, 4.6.5

edit, 10.5.6.1, 10.5.6.2

origin, 6.8.12, 23.2.10

move, 10.5.6.2

orthosteric, 5.7.7

new, 10.5.6.2

other selection, 4.6.19

search, 10.5.6, 10.5.6.3, 22.6.5, 22.6.6

outside, 23.5.9

phase angle P, 5.6.12

overlay, 22.3.3, 23.2.5, 23.4.6

phi, 6.8.5, 23.2.18

pH, 5.7.2, 10.19

phylogenetic, 8.7.8

pKa, 5.7.2, 9.13, 9.13.1

phylogeny, 8.7.8

package.activeicm, 7.13

pi, 5.3.2

packing, 5.4.1

cation, 5.3.2

pages, 20.7

pi, 5.3.2

pairwise, 10.37.5, 10.37.6

pi-pi, 5.3

apf score, 10.38

picking, 6

parallelization, 13.1.7

picture, 3.6.1.14, 4.15, 6.15.2, 7.6.3

passaro, 9.8.7

tips, 4.15

password, 10.10.5

chart, 18.4.8

paste, 10.4.11, 10.4.18, 18.1.35

pipi, 5.3.2

pca, 18.5

pka, 10.15

pdb, 3.6.1.7, 4.2.2, 4.16, 4.16.6, 4.19, 5.1.3, 10.7.1, 22.3, 23.2.24, 23.2.25, 23.4.4

planar, 5.6.7, 6.8.5, 23.2.18

chem gl, 10.7.3

angle, 5.6

iw, 10.7.2

angle, 6.9.2

dormat, 4.19

plane, 6.3.10, 6.13, 6.13.1, 6.14, 23.2.11, 23.2.19, 23.2.21

file, 23.4.3

faq, 23.2.21

html, 4.2.7

plddt, 9.8.3

preparation, 22.3.11

plot, 4.20, 4.20.8, 13.1.9.2, 18.4, 18.4.1, 18.4.4, 18.4.9, 18.4.11, 18.4.13, 18.4.14, 18.4.15, 18.4.16, 18.4.17, 18.4.18, 18.4.20, 18.4.21, 18.4.22, 18.4.23

search, 4.2.3, 4.2.4, 22.3.1

R group sar, 10.36.4

hyperlinks, 4.2.6

axis, 18.4.11

convert, 9.23.1

color, 18.4.14

recent, 3.6.1.18

columns, 18.4.6

search, 3.7.4, 4.2, 4.2.1

function, 3.6.9, 3.6.9.1

pdbsearchfield, 3.6.2.13

grid, 18.4.15

pdbsearchhomology, 3.6.2.15

header, 18.4.9

pdbsearchidentity, 3.6.2.14

inline, 18.4.22

pdbsearcsequence, 3.6.2.16

logarithmic, 18.4.12

peptide, 4.17, 9.16, 9.22, 12.12

mark, 18.4.13

docking, 12.12

mean median iqr, 18.4.23

modeling, 9.22

point label, 18.4.19

editor, 17.21

preferences, 4.20.8

percentage similarity, 8.7.15, 22.4.4

groups, 18.4.25

perspective, 3.6.3.9, 6.10.6

regression, 18.4.16

ph4, 10.5.6

selection, 18.4.18

draw 2d, 10.5.6.1

zoom translate, 18.4.17

3d, 10.5.6.2

axis, 18.4.15

search, 10.5.6.3

display, 18.4.15

pharmacophore, 10.3.35, 10.5.6.5, 22.8.2

grid, 18.4.15

2D, 22.6.6

inline, 18.4.22

3D, 22.6.5

logarithmic, 18.4.12

pmf, 23.5.6

problem, 23.1.14

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

with selection, 23.1.12

pocket, 4.9, 5.2, 5.2.2, 5.2.3, 5.7.7, 22.3.7, 23.2.14, 23.4.11, 23.5.10

prodrug, 10.26

conservation, 23.4.12

profile, 4.16.9, 8.3.8

properties, 5.9

project, 3.6.1.5, 12.13.4, 20.6, 22.6.4.6

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, 23.8.7

pocketome, 4.16, 4.16.1, 5.9

property, 10.4.9, 23.8.7, 23.8.8, 23.8.9, 23.8.10

pockets, 5.7.7

expression, 13.1.9.4

point label, 18.4.19

monitor, 10.4.9

portait, 4.20.6

protac, 12.14

post edit ligand, 17.5.8

protect, 7.6.8

screen, 13.1.9

protein, 5.5.6, 8, 9.8, 9.16, 23.4.5

postscript, 4.20.6

chain, 9.4

potential mean force, 13.1.4

complex, 9.8.1, 9.8.1.1

ppbatch, 12.13.9

health, 5.7.4

ppepitope, 12.13.7

model, 9.21

ppmaps, 12.13.8

preparation, 9.13, 9.13.1

pprefine, 12.13.11

protein docking, 22.10

ppresults, 12.13.10

tutorial, 22.10

pproc, 12.13.3

sculpting, 9.19

ppsetligand, 12.13.6

sequence, 10.4.17

ppsetproject, 12.13.4

structure, 5

ppsetreceptor, 12.13.5

analysis, 5.6

ppt, 7.12, 7.14, 23.3.3

closed cavities, 5.6.4

predict, 8.3.2, 10.21, 10.22, 11, 11.2, 18.6, 23.8.9, 23.8.12

contact areas, 5.6.3

disulfide, 9.18

distance, 5.6.6

metabolic oxidation, 16.7

find related chains, 5.6.1

predicting bioassays, 11.2

finding dihedral angle, 5.6.8

compound properties, 11.2

planar angle, 5.6.7

prediction binding, 9.14

rama export, 5.6.10

preferences, 4.20, 13.1.5, 23.2.24, 23.2.25

ramachandran plot, 5.6.9

preferred residues, 9.6

rmsd, 5.6.2

presentation, 7.6.5, 7.7, 7.12

surface area, 5.6.5

presentations, 7

similarity, 5.8

preserve, 23.8.6

tutorials, 22.3

press-and-hold to rotate, 10.4.8

analysis, 22.3.4

pretty view, 17.3.6

contact area, 22.3.5

primary aliphatic amines, 10.15

convert, 22.3.2

principal component analysis, 18.5

hydrogen bond, 22.3.6

regression, 11

icmpocketfinder, 22.3.7

components, 11.5

search, 22.3.1

print, 6.7, 18.4.20, 18.7.3

superimpose, 22.3.3

alignment, 8.7.4

superposition, 5.5

plot, 18.4.20

select, 5.5.1

alignment, 8.7.4

sites by apf, 5.5.6

printer.resolution, 4.20.6

superimpose 3D, 5.5.3

pro-drug, 10.26

grid, 5.5.5

probe, 12.2.1.1, 23.5.13

multiple proteins, 5.5.4

protein-protein, 5.7.6, 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, 22.10

start move structure, 4.4

docking refinement, 12.13.11

read pdb, 4.2

protein-proteindocking, 12.13.7

representation, 4.7

convert, 9.23.1

what is selected, 4.6.4

protonated, 23.4.15

display.distance, 6.9.1

protonation, 9.13, 9.13.1, 10.19, 12.1.4

start color, 4.8

charge, 9.13.1

quit, 3.6.1.19

state, 12.1.4

group, 10.28.7, 10.35.4

states, 5.7.2, 9.13, 9.13.1

table, 10.35.2

protonation_ph, 10.19

groups, 10.35.2

protonation_ph_charge, 10.19.2

r-group, 10.28.7, 10.35.2

protonation_ph_concentration, 10.19.1

decomposition, 10.28.7

protprot, 12.13

enumeration, 10.28.7

proximity, 6.3.3, 6.3.4

r-groups, 18.4.25

psa, 10.4.9, 10.11.9

racemic, 10.3.28, 10.20.5, 23.5.21

pseudorotation P, 5.6.12

radar, 18.4.6

analysis, 5.6.12

rainbow, 4.20.5, 6.8.16, 10.3.35, 23.2.38

phase angle, 5.6.12

ramachandran plot, 5.6, 5.6.10

psi, 6.8.5, 23.2.18

random forest, 11, 22.13

pubchem, 10.1

range, 6.10.7.2

publication quality images, 6.3.2

rapid isostere replacement, 13.4

puckering amplitude, 5.6.12

ratio.selection, 4.20.5

purple box, 3.6.3.23, 12.2.1.1, 17.9.1

dock ligand, 17.9

pyramid, 12.1.6

reactions, 10.8, 10.35.5

pyramidal, 12.1.6

reactive cysteine, 5.7.3

qm color by qm electrostatic potential, 15.6

reactivity, 10.11.3

introduction, 15.1

read, 3.6.1.3, 3.6.1.17, 4.18, 8.1, 10.3.1

minimimize, 15.2

chemical, 10.1

confromers, 15.3

spreadsheet, 10.3.1

set charges, 15.5

split, 11.1.1

torsion scan, 15.4

table, 18.1.2

hydrogen bond, 5.3.1

pdb, 4.2, 4.2.1

pdb chem gl, 5.1.3.2

table, 18

iw, 5.1.3.1

reagent, 10.35.5

qsar, 10.21, 10.22, 11.1, 22.13

rear, 6.3.10, 6.13.1

learn predict, 10.21

recent files, 3.6.1.17

predict, 10.22

pdb codes, 3.6.1.18

quad buffer stereo, 23.1

receptor, 5.2.2, 5.2.3, 5.3, 5.3.1, 10.6, 12.1, 12.6.2, 12.13.5, 12.13.7, 17.3.12, 22.12.1, 23.5.2, 23.5.14, 23.5.15

buffer, 23.1.7

considerations, 12.1.1

quality, 3.6.1.15, 4.20.5

flexibility, 17.15

quantum chemistry, 15

pocket, 17.3.1

mechanics, 15

surface, 17.3.1, 17.3.2

query, 9.1.2, 20, 20.3, 23.8.1, 23.9.5, 23.9.6

refinement, 9.20

molt, 19.4

flexibility, 22.12.2

processing, 10.5.3

recover, 3.6.2.11

setup, 10.5.1

cylinders, 8.7.16, 23.6.2

quick, 4.15

lines, 8.2, 23.6.1

image, 6.15.2

redo, 3.6.2.10, 10.4.11, 17.5.5

model multiple chain, 9.1.2.2

reference, 9.8.7

single chain, 9.1.2.1

refine, 9.9, 9.10

side chain, 9.10

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, 23.2.23, 23.2.34

region, 12.13.7

as a mesh object, 23.2.3

regression, 10.36.2, 11.1, 11.5, 18.4.16, 22.13

faq, 23.2.23

regul, 9.9

preferences, 4.20.9

regularization, 9.9, 9.23.3

style, 4.20.9

relationship, 11, 18.6

breaks, 6.1.3

covalent geometry, 12.2.1.3

cylinders, 6.1.3

relaxed ligand, 17.3.9

smooth, 6.1.3

reload, 12.4.1.4, 23.5.4

worm, 6.1.3

dock results, 12.4.1.4

ribbonColorStyle, 4.20.9

remove, 23.2.6, 23.2.7, 23.2.10

ribose pseudorotation, 5.6.12

salt, 23.8.14

pucker, 5.6.12

explixit.hydrogens, 10.12

ring, 5.6.12

salt, 10.12

conformation, 5.6.12

rename, 18.1.25

torsion angles, 5.6.12

column, 18.1.25

ride, 13.4

project, 3.6.1.9

gpu benchmark, 13.4.1.2

renumber, 9.2, 23.4.4

server setup, 13.4.1.1

reorder column, 18.1.29

setup, 13.4.1

replace chemical, 10.3.32

ridge, 13.5

replacement, 17.6

right, 4.13

group, 17.8

click, 4.13

report, 20.3

rigid, 10.37

representation, 3.6.3.19

substructure superposition to template, 10.37.2

residue, 4.20.7, 23.2.8, 23.4.15, 23.4.22

ring, 5.3.2, 10.4.3, 10.4.6, 10.5.1

alternative orientation, 22.3.11

stacking, 5.3.2

confidence, 9.8.3

rings, 10.3.28, 10.23, 10.37

content, 8.3.1

rmsd, 5.6, 5.6.2, 23.4.7, 23.4.8

names, 9.13, 9.13.1

rock, 3.6.3.15, 6.10.7, 6.10.7.1, 7

number selection, 23.2.36

speed, 6.10.7.2

pKa prediction, 5.7.2

root, 23.4.7

pka, 5.7.2

mean square deviation, 5.6.2

range, 4.6.18

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, 23.8.13

content, 3.6.4, 8.3, 8.3.1

chemical, 10.3.34

mutate, 23.4.13, 23.4.14

torsion, 6.12.6.1

residues, 5.2.2, 5.2.3, 23.2.14

when pasting, 10.4.8

resize, 6.3.9.1, 6.15.3

easy, 3.6.3.12

mesh, 6.3.9.1

speed, 6.10.7.2

resolution, 4.2.4

rotating fragment in editor, 10.4.8

restore, 3.6.2.11, 6.3.10, 6.13.1

rotation, 6.12.1

default, 23.1.9

rotational symmetry axis, 5.6.11

recent backup, 3.6.2.11

rough surface, 23.2.37

restrained docking, 12.5

row, 18, 18.1.22, 18.1.35, 18.1.45

restraint, 17.12.1, 17.12.2

flag, 18.1.13

restraints, 14.2

height, 18.1.7, 23.2.39

results, 12.13.10

mark, 18.1.13

retrieve columns, 23.5.24

hide, 10.3.8

from original database, 23.5.24

show, 10.3.8

molscreen, 16.1.2

scale, 4.20.5, 23.2.38

on cpu, 9.8.5

scan, 9.23.7

rundock, 23.5.16

r group, 17.7

rxn, 10.4.13

scan_pockets, 5.9

safari, 23.3

scarab, 20

sali, 10.36.5

add user, 20.5

bridge, 22.3.6

browse export data, 20.4

salts, 10.3.18

installation, 20.1

sample, 9.21, 10.37

new project, 20.6

double bond cis trans, 12.2.1.3

pages, 20.7

ligand pocket, 9.20

query, 20.3

peptide, 9.22, 9.23.12

upload data, 20.2

protein, 9.21, 9.23.11

scare, 12.6.4

racemic centers, 12.2.1.3

scatter, 13.1.9.2

sar, 10.28.7, 10.36, 18.4.25

score, 13.1.8, 17.4, 22.8.3, 22.8.5, 23.5.7, 23.5.8, 23.5.18

analysis, 10.36

threshold, 13.1.4

table, 10.36.3

screen, 10.38, 22.8.4, 22.9, 22.11.1

save, 4.19, 6.3.11, 6.10.7.4, 8.1.5, 10.2.3, 18.4.21, 18.7.3, 23.2.33

screening, 13.1, 13.1.1, 13.1.2, 13.5, 14.4, 22.12

SMILES, 10.4.15

screenshot, 6.16, 6.16.2

alignment, 8.7.3

movie, 6.16.2

PDB, 4.19

script, 4.17, 7.6.4, 7.6.5, 23.4.19, 23.10, 23.10.1, 23.10.2, 23.10.3

pdb, 4.19

sculpting, 9.19

chemical mol, 10.4.13

sdf, 9.8.6.1, 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, 17.10, 19.1, 20.2, 22.11.2, 23.9.3, 23.9.4

spreadsheet workspace, 10.2.1

to hitlist, 12.4.1.6

to chemical spreadsheet, 10.4.14

search, 5.8, 10.10, 10.10.4, 19.2, 20.3, 23.9.6

docked ligand, 17.20

chembl, 4.16.2

file, 4.19

drugbank, 4.16.7

hits, 17.5.7

filter, 10.5.2

image plot, 18.4.21

in workspace, 3.6.2.4

ligand receptor complex, 17.20

pdb, 4.2.1

object, 4.10

ligand code, 4.16.6

pdb, 4.19

pocketome, 4.16.1

project icb, 4.11

pubchem, 4.16.8

sequence, 8.1.5

surechembl, 4.16.3

slide, 7.4

tab field, 4.2.4

smiles string, 10.4.15

pdb chemical, 4.2.2

table, 18.1.21

sequence, 4.2.3

spreadsheet, 17.5.7

tautomer, 10.5.3

tree, 18.7.3

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, 5.7.1, 23.2.20

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, 18, 18.1.45, 23.4.22

project, 3.6.1.8, 3.6.1.9, 3.6.1.10, 4.11

a tree branch, 18.7.2

table.view, 18.1.8

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, 17.8

neighbors, 4.6.15

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, 9.8.1, 10.4.17, 22.3, 22.4, 22.4.4, 23.4.12, 23.6, 23.6.1

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, 18.7.2

pattern, 4.2.3

atom, 4.6.3

reordering, 8.7.8

graphical, 4.6.3

secondary structure, 8.2, 23.6.1

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, 18.4.18, 18.7.2, 18.7.4, 23.2.4, 23.2.6, 23.2.7, 23.2.8, 23.2.13, 23.2.32, 23.4.9, 23.4.10, 23.4.22, 23.5.14

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, 23.2.25

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, 18.1.23

error, 23.1.17

filter, 3.6.2.5, 4.6.8

set, 10.3.31, 23.4.21

graphical, 4.6.16

formal charges, 10.15

invert, 3.6.2.6, 18.1.23

server, 23.1.17

level, 3.6.3.3

bond type, 9.23.5

mode, 3.6.3.4

charges, 9.23.6

near atoms, 3.6.2.8

chirality, 9.23.5

neighbors, 3.6.2.5, 3.6.2.8, 4.6.15, 4.6.17

disulfide, 9.11, 23.4.17

object, 4.6.11

bond, 9.23.5

other, 4.6.19

formal charge, 9.23.5

properties, 3.6.2.5

tether, 9.23.5

range, 18.1.23

types, 9.23.6

residue, 3.6.2.5

setAPFparams, 23.8.12

row, 18.1.23

setup, 12.13.6

sphere, 4.6.15

ligand receptor, 17.1

spherical, 3.6.2.8

shade, 8.7.7, 8.7.7.1

superposition, 5.5.1

alignment, 22.4.4

table, 4.6.19, 18.1.23

shading, 6.3.12

elements, 18.1.23

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, 23.2.20

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, 18.1.39

organized network, 10.30

hide column, 18.1.39

by side, 10.3.29

spec, 3.7.2

error, 23.1.19

specifications, 23.1.5

stereo, 3.6.3.6

specs, 1

chain refinement, 17.14

faq, 23.1.5

chains, 9.10

speed, 6.10.7.2

side-by-side, 23.1.19

sphere, 23.4.11

side-chain optimization, 9.20

spherical, 23.4.9, 23.4.12

sampling, 12.13.11

split, 10.36.1

side-chains, 12.6.1

spreadsheet, 10.20.2

sigmaLevel, 5.4.6, 5.4.7

square, 23.4.7

similarity, 10.31

stability, 9.15, 22.5.3, 22.5.4

simulation, 14, 14.1, 14.2, 14.3, 14.4, 23.9.8

stack, 9.8.2, 9.21, 9.23.18, 12.4, 12.13.10, 23.9.8

length, 23.5.12

calculations, 9.23.18

simulations, 23.7

stacking, 5.3.2

single, 10.4.10

standalone hitlist, 12.4.1.3

chain, 9.1.2.1

standard table, 18.1

single-point energy, 15

standardize, 10.12

singlet, 10.4.7

table, 10.12

sites, 5.5.6

start, 10.10.2

size, 5.3.1.1

startup, 23.10.2

sketch accents, 6.10.3

static, 23.4.8

markush, 10.35.1

stereo, 4.20.6, 6.6, 10.3.28, 10.4.2, 23.1, 23.1.6, 23.1.7, 23.1.14

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, 23.2.16

stereohard faq, 23.1.6

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, 23.2.31

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, 23.2.22

navigation, 7.3.2

current view, 3.6.3.19

show, 7.3

faq, 23.2.22

blend, 7.5

strain, 5.7.4, 6.12.6.1, 10.17, 10.27, 10.27.2, 12.1.10, 17.4

edit, 7.4.1

strip, 23.4.9

effect, 7.5

structure, 5.4.3, 11, 18.6, 22.3, 23.4

smooth, 7.5

analysis, 5.6.12, 22.3.4

transition, 7.5

ensemble, 9.23.14

slides, 6.16.1, 7, 7.1, 7.3, 23.2.30

prediction, 9.8

smiles, 10.4.9, 10.11, 10.20, 10.20.3, 10.20.4

preparation, 9.20

smooth, 6.3.9.3

representation, 6.1

surface, 23.2.37

smiles, 10.20.4

solid, 6.3.9.3

structure-based, 13

solvent.accessible.area, 23.4.19

structures, 10, 10.1

sort hitlist, 13.1.9.1

style, 4.20.5

table, 3.6.10.4

substituent, 10.9.1, 10.9.2, 10.35.2, 17.5.2

sorting, 13.1.9.1

substructure, 10.10.4, 10.13, 10.37.1, 10.37.2, 12.7, 23.8.1, 23.9.5

compounds, 18.7

template, 17.12.3

sp3, 10.11.2

alerts, 10.13

pucker analysis, 5.6.12

print, 18.1.19

puckering, 5.6.12

rename, 18.1.15

ring puckering, 5.6.12

rightclick, 18.1.14

sulfur, 9.11

row height, 23.2.39

superimpose, 3.6.8, 5.5.2, 5.5.6, 10.37.4, 22.3.3, 23.2.5, 23.4.6, 23.4.7, 23.4.8

save, 18.1.3

3D, 5.5.3

selection, 18.1.3

Calpha, 5.5.3

search, 18.1.9

arrange.grid, 5.5.5

select, 18.1.23

backbone, 5.5.3

setup, 18.1.18

heavy atoms, 5.5.3

sort, 18.1.42

multiple, 5.5.4

split fragments, 10.3.33

superposition, 10.37, 10.37.1, 10.37.2, 10.37.5, 10.37.6, 22.3.3, 22.8.1

view, 18.1.5

surface, 3.7.1, 4.20.5, 5.2.2, 5.2.3, 6.1.6, 6.3, 6.3.3, 6.3.4, 23.2.16, 23.2.37, 23.4.19

save, 18.1.8

area, 5.6

zoom translate, 10.3.30

area, 5.6.5

action, 18.1.47

surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5

alignment, 18.1.12

surrounding, 23.4.11

append, 18.1.43

swissprot, 8.1, 8.5

clone, 18.1.16

sxstrace, 23.1.19

color, 18.1.10

symmetric oligomer, 9.1.3

column, 10.3.4, 18.1.26, 18.1.32, 18.1.39

symmetry, 5.4.1, 5.4.3, 22.3.8, 22.3.9

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, 18.1.47

tab, 18.1.2, 18.1.21

delete, 18.1.14, 18.1.17

pdb, 3.7.4

display, 23.10.4

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, 17.10, 18, 18.1.6, 18.1.35, 18.1.40, 18.1.45, 18.4, 18.4.1, 18.4.4, 18.4.9, 18.4.11, 18.4.13, 18.4.14, 18.4.15, 18.4.16, 18.4.17, 18.4.18, 18.4.20, 18.7.1, 23.4.19, 23.8.4, 23.8.5, 23.8.7, 23.8.8

double.click, 18.1.47

alignment, 18.1.12

edit, 10.3.17

clone, 18.1.16

excel, 10.3.10, 18.1.20

color, 18.1.10

filter, 10.3.12, 18.1.43

column format, 18.1.40

find-replace, 10.3.13

copy, 18.1.36, 18.1.37

to screen, 18.1.4

delete, 18.1.17

font, 18.1.11

edit, 18.1.24

foreground, 23.10.4

filter, 18.1.43

grid lines, 18.1.4

find, 18.1.9

hide, 18.1.39

replace, 10.3.32

hyperlink, 10.3.15

font, 18.1.11

insert, 18.1.33

size, 23.2.1

join, 3.6.10.5

grid, 18.1.5

label, 10.3.14

histogram, 18.4.1

landscape, 18.1.18

insert, 18.1.26

mark, 10.3.14

layout, 18.1.5

merge, 3.6.10.5, 10.3.23, 10.32

learning, 18.6

mouse, 18.1.47

mark, 18.1.13

name, 18.1.15

row, 18.1.13

new, 18.1.1

mouse, 18.1.47

options, 18.1.14

navigation, 18.1.4

orientation, 18.1.18

new column, 18.1.26

portrait, 18.1.18

plot, 18.4

print, 10.3.11, 18.1.4, 18.1.19

rename, 18.1.15

balloons, 18.4.26

right click, 18.1.14

torsion, 6.12.6, 6.12.6.1, 9.23.7, 10.17, 17.5.4, 23.4.16

row, 18.1.33

analysis, 10.16

rows, 3.6.10.7

angles, 6.12, 6.12.6

save, 10.3.9, 18.1.3, 18.1.4, 18.1.21

free strain, 10.17

scale, 18.1.18

scan, 9.23.7, 15

scroll, 18.1.4

toxscore, 10.11.3

sdf, 10.3.9

trace, 6.1.10

select, 18.1.23

transition.blend, 23.2.31

setup, 18.1.18

transitions, 7, 23.2.30

sort, 3.6.10.4, 10.3.5, 18.1.42

translate, 4.4, 6, 6.12, 10.3.30

standard, 18.1

translation, 6.12.3, 8.3.3, 18.4.17

view, 10.3.29

transparent, 6.3.9.3

width, 18.1.4

background, 6.15.3

tables, 10.31, 18

ribbon, 23.2.3

tag, 4.6.21, 17.5.7, 18.1.46

surface, 23.2.37

tags, 4.6.21

tree, 8.7.8, 10.28.7, 18.7.2, 18.7.3, 18.7.4

m, 5.6.12

branch swapping, 8.7.8

tautomer, 10.24, 23.4.15

distance, 10.28.3

tautomers, 10.24

edit, 10.28.4

temperature, 5.7.5

reorder, 10.28.3

template, 9.1.2, 10.4.6, 10.37

triplet, 10.4.7

docking, 23.5.3

trouble shooting, 23.1.11

templates, 10.4.6

trouble-shooting, 23.1.12

terminal, 10.3.28

truncating a mesh object, 23.2.15

font size, 23.2.1

crash qlock, 23.1.13

tether, 12.5, 17.12.1, 17.12.2

tsv, 18.1.21

text, 4.20.7, 7.6, 7.6.1, 7.6.7, 10.3.28, 10.10.4, 18.4.24, 23.9.6

tut analyze alternative orientations, 22.3.11

search, 10.5.4

occupancy, 22.3.10

texture, 3.7.6

symmetry, 22.3.9

thoroughness, 10.23, 10.37, 23.5.12

multiple receptor, 22.12.1

three, 10.3.24, 23.8.6

tut3, 22.5

threshold, 4.20.5

tut3e, 22.3.12

tier, 4.14

tut5a, 22.9.1

time, 23.5.11

tut5b, 22.9.2

machine, 23.1.15

tut5c, 22.11.1

tissue, 4.16.9

tut5e, 22.11.2

racemic, 10.20

tutorial 2D pharmacophore, 22.6.6

tools 3D, 3.6.6

3D pharmacophore, 22.6.5

analysis, 3.6.7

chemical clustering, 22.6.3

append rows, 3.6.10.7

search, 22.6.2

extras, 3.6.9

molecular documents, 22.2

plot function, 3.6.9.1

sequence alignment, 22.4

superimpose, 3.6.8

link, 22.4.2

table, 3.6.10

load sequence, 22.4.1

Learn, 3.6.10.1

sequence conservation, 22.4.3

clustering, 3.6.10.3

tutorials, 22

merge, 3.6.10.5

two, 10.3.24, 23.8.6

predict, 3.6.10.2

ubuntu, 23.1.18

tooltip, 18.4.26

ultra large library, 13.5

undisplay, 4.5, 6.1.7, 23.2.10, 23.2.32

visualize, 10.30

box shade font, 8.7.7.1

apf fields, 17.3.11

undisplay-all, 3.6.3.1

chemical space, 10.30

origin, 6.8.12

ligand strain, 17.3.10

undo, 3.6.2.9, 4.20, 10.4.11, 17.5.5

vls, 12.6, 12.6.3, 13, 13.1, 13.1.6, 13.1.7.2, 13.1.9.4, 13.3, 14.4, 22.11.2, 23.5.7, 23.5.8, 23.5.24

redo, 17.5.5

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, 5.4.3

getting started, 13.1.2

units, 23.5.1

histogram scatter plot, 13.1.9.2

unix, 23.10.2

introduction, 13.1.1

unsatisfied hydrogen bonds, 17.3.8

preferences, 13.1.4

unusual peptide, 4.17

results, 13.1.8

upload, 20.2

run, 13.1.6

use activeicm, 7.12

score, 12.1.9

user, 10.10.5, 20.5

visualization, 13.1.11

defined groups, 17.5.3

results, 13.1.8

modifiers, 17.5.3

volume, 10.4.9

user-defined groups, 10.4.5

water, 9.23.17, 12.1.8

van der waal, 6.8.15

waters, 9.23.17

variable, 4.20.7, 23.2.8

wavefront, 3.7.6, 6.3.11, 6.7

verbose, 10.23

weak, 23.4.20

large sdf files, 10.1.2

web, 22.2

vicinity, 10.23

browser, 3.6.1.12

video, 2, 6.16, 6.16.1, 6.16.2

weight, 10.11, 23.8.7, 23.8.10

view, 3.6.3.19, 7.3.1, 10.3.28, 23.2.22, 23.9.8

weighted, 18.7.1

animate view, 3.6.3.15

weights, 9.8.4

center, 3.6.3.20

update, 9.8.4

color background, 3.6.3.18

width, 18.1.22

dock results, 12.4

window, 4.14

fog, 3.6.3.5

windows, 4.14.1, 10.10.1

macroshape, 3.6.3.22

wire, 3.7.1, 4.20.5, 6.1.1, 23.2.4, 23.2.21

menu, 3.6.3

wireBondSeparation, 4.20.1

mesh clip, 6.13.1

wohlwend, 9.8.7

perspective, 3.6.3.9

working directory, 23.5.23

selection level, 3.6.3.3

workspace, 4.5, 5.1.3.1, 10.7.2

mode, 3.6.3.4

panel, 4.5

shadow, 3.6.3.13

selection, 4.6.9

sketch accents, 3.6.3.14

navigation, 4.6.10

slide show, 7.3.1

write, 4.15, 4.19, 18.4.21, 23.9.4, 23.9.7

tools, 3.6.3

alignment, 8.7.3

tree, 18.7.4

excel, 10.2.3

undisplay all, 3.6.3.1

image, 3.6.1.15, 23.1.20

stach, 9.23.15

images, 6.15

virtual, 13.1, 13.1.1, 13.1.2, 22.9, 22.11.1

pdb, 4.19

ligand screening, 16

image, 3.6.1.15

screen, 13.3, 13.4

object, 4.10

screening, 13, 13.2

picture, 3.6.1.15

examples, 22.11

project, 3.6.1.8, 4.11

virus, 5.4.3

table, 18.1.3

ray, 3.6.5

xi, 6.8.5, 23.2.18

xls, 10.2.3

xlsx, 10.2.3

xml, 20.2

xstick, 6.1.2, 23.2.21

xyz, 23.2.10

youtube, 2

zoom, 4.4, 6, 6.12, 6.12.4, 10.3.30, 18.4.17

τm, 5.6.12