ICM User's Guide: Index

modify group, 9.12.2

Alpha-Helix Stabilization, 17.21

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

Altona-Sundaralingam pseudorotation, 5.5.12

Chemical Label, 6.8.11

Area, 9.22.18, 23.2.26

Interaction Diagram, 17.3.7

Atom Single Style, 4.20.3

bioisostere, 10.9.1

Atomic Property Fields, 11.4, 22.14

chemical label, 6.8.11

B3LYP, 15

from PDB, 10.1.1

Bad Groups, 23.8.7, 23.8.10

interaction diagram, 10.6

Baell, 10.4.9

screening, 16

Beep, 4.20.11

to 3D, 10.20, 10.20.3

Beta-Catenin, 17.21

depiction, 10.20.2

Bioactive Conformation, 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

Blast, 23.2.25

QSAR, 10.38.4, 11.4, 22.14

BlastDB Directory, 4.20.2

chemical, 10.4.16, 10.20.1

alphas, 6.8.3

interactive ligand editor, 3.7.5

C-alpha backbone, 5.5.11

ligand editor, 17.3.4

C2′-endo pucker, 5.5.12

object, 6.3.9

C3′-endo pucker, 5.5.12

pharmacophore, 13.3, 17.3.11

CHEMRIYA, 13.5

print, 6.7

COLLADA, 3.6.1.7

printing, 6.7

CPK, 3.7.1

screening, 16

CYM, 9.12, 9.12.1

stereo, 6.6

CYS, 9.12, 9.12.1

visualization, 5.5.11

ChEMBL, 4.16.2, 10.1

3DMOLT, 19.5

Chemical Cluster, 22.6.3

3DQsar, 11.4

Search, 22.6.2

3D_Similarity_PDB_Search, 5.7

CisTransAmide Angle, 13.1.9.4

3Dqsar tutorial, 22.14

Clash Threshold, 4.20.10

bioisostere, 10.9.2

Computational Chemistry, 17.21

predict, 5.6

Computer-Aided Drug Discovery (CADD), 17.21

helices strands, 5.6.1

Covalent Geometry., 17.21

local flexibility, 5.6.5

DFT, 15

protein health, 5.6.4

DILI, 10.11.5

tools identify ligand binding pocket, 5.6.7

DNA, 4.17, 8, 8.3.3

oda, 5.6.6

Decomposition, 10.36.3

4D, 12.6.2, 22.12.1

Design Evolution, 12.10

dock, 17.15

Dimer, 5.5.11

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, 5.5.12

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, 9.12, 9.12.1

Eintl, 12.1.10

ARN, 9.12, 9.12.1

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

ASP, 9.12, 9.12.1

Extended Amino Acids, 17.21

ASPH, 9.12, 9.12.1

FILTER.Z, 4.20.2

Acetyl Cap, 17.21

gz, 4.20.2

ActiveICM, 3.6.1.12

uue, 4.20.2

Alignment mode, 5.5.11

FTP.createFile, 4.20.11

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, 9.22.16

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, 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

HBA, 13.1.10, 23.8.7, 23.8.10

light, 4.20.3

HBD, 13.1.10, 23.8.7, 23.8.10

lightPosition, 4.20.3

HF, 15

mapLineWidth, 4.20.3

HID, 9.12, 9.12.1

occupancy Radius Ratio, 4.20.3

HIE, 9.12, 9.12.1

HIS, 9.12, 9.12.1

Plot, 5.5.12

HTTP.proxy, 4.20.11

Internal Coordinates Table, 9.22.13

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, 9.12, 9.12.1

Helicon Peptide, 17.21

LYS, 9.12, 9.12.1

Homodimer, 5.5.11

LigStrain, 17.21

Homologous chains, 5.5.11

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, 5.5.12

MPO, 10.34

graphics crash, 23.1.11

Mac, 23.1.15

object, 5.6.2, 9.19

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, 9.12

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

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, 17.3.7

NCBI, 23.2.25

Interactive Ligand Editor, 17.21

NH2 Cap, 17.21

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, 5.5.12

complex, 5.5.11

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, 5.5.12

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, 5.3.3, 5.7, 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, 5.4.2, 9.22.18

convert, 5.1.2

RMSF, 9.22.18

PFAM, 3.6.1.7

RNA, 4.17

PLOT.Yratio, 4.20.8

backbone conformation, 5.5.12

color, 4.20.8

chain analysis, 5.5.12

date, 4.20.8

conformation, 5.5.12

draw Tics, 4.20.8

pucker, 5.5.12

font, 4.20.8

structure analysis, 5.5.12

fontSize, 4.20.8

sugar conformation, 5.5.12

labelFont, 4.20.8

RTCNN, 12.1.9, 12.4.3.1

lineWidth, 4.20.8

Score, 17.21

logo, 4.20.8

Ramachandran Plot, 5.5.9

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

PNG, 3.6.1.15, 4.15, 6.16, 6.16.2

Rotation angle, 5.5.11

PROPKA, 5.6.2

Rotational symmetry axis, 5.5.11

PROTAC, 12.14

SALI, 10.36.5, 22.6.11

PSA, 10.11.9

SAR, 11, 16.6, 18.4.25, 18.6

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

acceptor, 10.4.9, 10.38.1

labelOffset, 4.20.7

active, 7.7, 23.3.3

wrap Comment, 4.20.7

activeICM, 7.8

SLIDE.ignore Background Color, 4.20.4

activeicm, 7.7, 7.12, 7.14, 7.14.1, 23.3

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, 17.21

activity, 11, 18.6

Show Res Code In Selection, 4.20.7

cliff, 10.36.5, 10.36.6, 22.6.11

Sidechain Optimization, 17.21

tutorial, 22.6.11

Smiles, 23.8.7, 23.8.10, 23.8.11

add database, 10.10.3

South conformation, 5.5.12

new data, 10.3.7

Special Cases, 10.34.1.1

to table, 17.5.7

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, 23.2.39

SureChEMBL, 4.16.3

administration, 10.10.5

Swissprot, 3.6.1.7

advanced alignment selection, 8.7.14

Dat, 4.20.2

ai, 17.18

link, 18.1.40

decoration, 17.18

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, 17.21

color 2D scaffold, 10.14

Tools Analysis, 5.5.12

dna protein, 8.6.4

Torsion Minimization, 17.21

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, 22.4.4, 23.4.12, 23.6, 23.6.2

Ultra Large Libraries, 19.5

annotation tutorial, 22.4.4

Uniprot, 18.1.40

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, 23.2.1

Label Style, 4.20.7

format, 8.7.11

Volume, 23.8.7, 23.8.10

gaps, 8.7.11

Change, 13.1.9.4

image, 8.7.2

Water Radius, 4.20.10

profile, 22.4.4

Wilson, 10.36.2

reorder, 8.3.12

Wire Style, 4.20.1

search, 8.7.12

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, 5.4.6, 5.8, 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, 5.6.7

applying prediction models, 11.2

alpha, 3.7.2

area, 5.5.3, 5.6.6, 12.13, 12.13.2, 12.13.3, 22.3.5

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, 23.2.8

amidinium, 10.15

as2_graph, 4.6.5

amino acid, 4.17, 9.12

as_graph, 23.2.8

acids, 9.12.1, 10.4.6

asparagine, 9.22.2

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, 5.6.1

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, 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

store, 6.10.7.4

property field, 10.37.5, 10.37.6, 17.3.11

animations, 7

score, 10.38.2

annotate, 4.6.21, 10.13

fields, 5.4.6, 5.8, 10.38, 10.38.1, 10.38.3, 13, 22.8

alignment, 8.7.6

attachment, 10.4.3, 10.5.1

by substructure, 10.13

point, 10.35.4

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, 5.3.3

available properties, 10.11.1

biomolecule, 3.6.5, 5.3.3, 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

title, 18.4.10

bond, 5.1.3, 5.2.4, 5.2.4.1, 5.2.4.2, 9.10, 10.4.10, 23.4.1, 23.8.7, 23.8.10

b-factor, 5.6.5, 22.3.10

covalent, 23.4.2

coloring scale, 23.2.38

type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3

backbone, 6.1.10, 23.2.13

bonding, 6.1.8

background, 6.4.2, 6.4.3

preferences, 4.20.1

color shortcut, 23.2.2

box, 4.20.7, 6.8.16, 8.7.7, 8.7.7.1, 23.5.9

images activeicm, 7.15

alignment, 22.4.4

image, 6.4.3

size, 17.9.1

backup, 3.6.2.11

browse, 10.3.31, 12.4.1, 20.4

bad, 10.11

mode, 10.3.31

groups, 10.4.9

molt, 19.2

ball, 4.20.5

stack, 9.22.15

and stick, 3.7.1

build, 6.10.7.1

balloon, 18.4.26

2D qsar, 11.1.2

bases, 10.4.6

homology model, 9.1.2

basicsel, 4.6.2

hydrogens, 9.22.5

set, 15

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, 23.5.2

bayesian classifier, 11

properties, 10.11

bbb, 10.11.6

sequence similarity, 8.7.15

beep, 23.2.35

startup, 23.10.2

begin docking simulation, 12.3

carbon, 23.2.4, 23.2.5

best, 10.3.34

carboxylic acid, 10.15

bicyclics, 10.4.6

cartesian, 10.23

binding, 22.5.3, 23.2.14, 23.5.2, 23.5.10

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, 23.2.27, 23.2.28

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, 17.3.13, 18.1.40, 23.4.22

menu, 3.6.4

on ligand, 17.3.13

secondary structure, 8.3.2

and representative members, 18.7.2

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, 9.12.1, 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, 9.22.1, 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, 9.12, 9.12.1

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

fragments, 10.3.33

duplicates, 10.33

group, 10.4.5

remove.redundant, 10.33

groups, 10.4.5, 10.4.8

chemlib.so, 23.1.3

modifiers, 10.35.2

chemspace, 10.5.5

properties, 22.6.4

append, 22.6.4.4

right click, 10.4.3

build visualize, 22.6.4.1

search, 10.5, 13.4

compare, 22.6.4.8

filter, 10.5.2

delete row, 22.6.4.3

text, 10.5.4

distinguish, 22.6.4.7

sketch, 22.6.1

export, 22.6.4.5

space, 10.30

project, 22.6.4.6

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

select, 22.6.4.2

compare, 10.3.22

chi, 6.8.5, 23.2.18

template, 10.3.2

chimeric ligands, 12.9

spreadsheets, 10.3

chiral, 10.25, 12.1.3

considerations, 12.1.3

plot, 18.4.6

chrome, 23.3

row width, 18.1.22

cis trans proline, 22.5.2

statistics, 18.1.32

clash, 4.20.5, 6.8.15

visibility order, 18.1.28

volumes, 13.1.11

color, 18.1.10

classes, 10.3.28

hide, 10.3.8

classification model, 16.5

show, 10.3.8

clear display and planes, 3.6.3.2

combinatorial chemistry, 10.35

selection, 4.6.6

library, 22.6.8

planes, 3.6.3.2

combine, 3.6.10.5

click, 4.13, 6.11, 6.12

display style, 4.20.9

clip, 6.3.10, 6.13.1, 23.2.11

command, 23.5.16

clipboard, 6.15.3, 18.7.3

line, 23.2.32

clipping, 23.2.19

commands, 23.10.1

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, 17.23

tables, 10.31

downstream cluster, 10.28.5

compatible, 3.6.1.10

project, 17.23

complex, 10.6, 13.1.9.3

cavities, 5.6.7

compound, 4.2.4, 10.24, 18.2

cloud, 13.1.7, 13.1.7.2

compounds, 23.9.3

cluster, 9.22.18, 13.1.7, 13.1.9.5, 18.7.1

compress, 4.20.6

stack, 9.22.18

compressed, 18.1.6

representative.center, 10.28.2

table view, 18.1.6

clustering, 18.7, 22.6.3

conditions, 10.5.2

cns, 10.34

gen, 10.23

collada, 3.7.6, 6.3.7

configuration error, 23.1.19

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, 18.1.45, 18.7.4, 23.2.4, 23.2.5, 23.2.16, 23.2.20

conformation, 9.22.18, 10.23, 12.6.2

alignment, 8.7.9

conformational entropy, 10.27

background, 6.4.2

stack, 15

by, 6.4

conformations, 23.9.8

alignment, 8.8

conformer energies, 15

chemical, 10.3.35

conformers, 10.23

faq, 23.2.20

connect, 6.3.9.1, 6.12, 6.12.7

key, 23.2.38

object, 6.12.7

scale, 23.2.38

connectivity, 10.4.3, 10.5.1

surface by proximity, 6.3.3

consensus, 10.38, 22.8.2

selection, 6.3.4

pharmacophore, 10.38.1

table, 10.3.27

construct, 3.6.1.1, 6.10.7.1

2D sketch, 10.5.6.5

molecule, 3.6.1.1

background, 3.6.3.18, 6.4.2

object, 3.6.1.1

distance, 6.8.10

contact, 5.5, 5.5.3, 22.3.5

mesh, 6.3.9.3

surface, 6.3.2

table, 10.3.27

contacts, 6.3.3, 6.3.4, 10.6, 13.1.9.6, 17.3.12

coloring, 6.4.1

contour, 5.3.6, 5.3.7

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

convert, 5.1.2, 10.20.1, 10.20.5, 23.8.5

annotation, 18.1.41

chemical, 10.3.24

order, 18.1.29

2D 3D, 10.7

from pdb, 5.1.3

fragments, 10.13

local database, 3.6.1.6

label, 6.8.8

pdb, 5.1.2, 22.3.2

rotation, 6.12.2

chem, 10.7.1

customized MPO score, 10.34.1

smiles to 2D, 23.8.11

cut, 18.1.35

local.database, 3.6.1.6

vertical alignment block, 8.3.11

smiles, 10.20, 10.20.3, 10.20.4

cyclic peptide, 9.21

coordinates, 10.1.3

cys, 5.6.3

copy, 10.3.25, 10.4.11, 10.4.18, 10.5.6.2, 18.1.35

cysteine reactivity, 5.6.3

cell, 18.1.36

damaged skin, 23.1.12

chemical, 10.3.25

dash, 23.2.12

loop, 9.5

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

paste row, 18.1.35

file format, 13.1.3

row, 18.1.36

search and alignment, 8.4

rows, 18.1.44

databases, 23.9.3

selection to table, 18.1.37

novo, 12.10

chemical, 10.3.16

design, 12.9

covalent, 17.10.1

decompose.library, 22.6.9

bond, 5.6.3, 22.9.3

decomposition, 10.35.4, 10.36.1, 18.4.25

docking, 12.8, 12.8.1, 17.16, 22.9.3

decoration, 17.18

tutorial, 22.9.3

default, 4.14

cpk, 6.1.5, 23.2.21

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, 5.6.7

column, 18.1.38

crystal, 5.3.2

distance.label, 6.9.4

crystallographic analysis, 5.3

label, 6.8.9

biomolecule, 5.3.3

row, 18.1.38

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, 23.2.27, 23.2.28

symmetry packing, 5.3.1

functional theory, 15

tools, 22.3.8

depth, 6.3.12, 6.10.5

cell, 3.6.5

deselect, 23.2.7

neigbor, 5.3.1

design loop, 9.4, 9.22.10

neighbors, 3.6.5

deviation, 23.4.7

crystallography, 5.3.4, 5.3.6, 5.3.7, 23.2.27, 23.2.28

dfa, 16.3.3

csv, 10.2.3, 18.1.2, 18.1.3, 18.1.21, 20.2

dfz, 16.3.2

current, 23.2.22

dialog, 7.6.5

slide, 7.13

diffuse, 3.7.2

curves, 18.4.5

dihedral, 5.5.8, 6.8.5, 23.2.18

custom, 6.12, 10.3.3, 10.37

angle, 5.5

actions, 18.1.40

dimensional, 23.8.6

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, 5.2.4, 5.2.4.1, 5.2.4.2, 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, 9.10, 9.17

delete distances, 6.9.4

bonds, 9.17

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, 5.6.6, 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, 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, 12.4.6

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

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, 23.5.13

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, 17.12.3

origin, 6.8.12

tutorials, 22.9

potential, 3.6.3.21

waters, 12.1.8

representations, 3.7.1

background, 23.5.19

restraints, 6.8.14

batch, 12.3.2

ribbon, 6.1.3

conformations, 23.5.20

skin, 6.1.4

flexible.rings, 23.5.20

status, 23.2.32

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, 23.5.20

distance, 5.5, 5.5.6, 6.8.10, 6.9, 10.31, 23.2.12, 23.4.8, 23.4.10

score, 12.4.3

template, 12.7

editpdbsearch, 3.6.2.12

document, 7.6.4, 7.6.5

eds, 5.3.4, 5.3.6, 5.3.7

navigation, 7.6.7

effect of mutation, 9.15, 9.16

documents, 6.15.3

on binding tutorial, 22.5.3

dollar, 23.10.3

example2, 22.5.3.1

donator, 10.4.9

stability tutorial, 22.5.4

envelope, 3.7.1

effort, 10.23, 10.37, 23.5.12

surface, 4.20.5

electron, 5.3.4, 5.3.6, 5.3.7, 23.2.27, 23.2.28

dotted line, 6.1.3

denisty map, 5.3.5

lines, 23.2.34

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

double, 10.4.10

contour, 3.6.5

doublet, 10.4.7

electrostatic coloring scale, 23.2.38

download, 23.1.1, 23.9.3

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

easy rotate, 3.6.3.12

powerpoint, 7.7, 7.8, 7.9, 7.10

ecfp, 11.3

empty hostid, 23.1.18

edit, 5.2.4.1, 17.5.8, 23.8.3

enamine, 10.5.5

2D, 17.5.1

real, 13.5

add sequence, 10.4.17

enantiomer, 23.5.21

alignment, 8.7.1

enantiomers, 12.1.3

chemical moledit, 10.3.26

endocyclic torsion angles, 5.5.12

ligand, 17.5, 17.5.1

energy, 5.6.4, 6.8.15, 10.27, 10.27.2, 12.4.2, 23.5.1, 23.5.2, 23.9.8

2D, 17.5.1

circles, 13.1.11

editor preferences, 17.2

maps, 12.2.1.1, 12.2.1.2

multiple substituents, 17.5.2

minimization, 15

tools, 3.6.2.17

terms, 9.22.19

menu, 3.6.2

ensemble, 12.6.2

molecular document, 7.6.1

calculations, 9.22.18

molecule, 10.4

entropy, 10.17, 10.27.1

molt, 19.3

enumerate formal charge states, 10.18

selection, 3.6.2.5

reaction, 22.6.10

slide, 7.4.1

enumeration, 10.35.4

table row, 18.1.24

eps, 10.2.6

molecule, 10.3.26

epsilon, 23.4.15

structure, 10.3.26

eraser, 10.4.11

editor, 23.4.12

errno, 23.1.3

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, 5.5.10, 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

path, 23.3.3

hydrogen bond acceptors, 23.8.17

alignment secondary structure, 23.6.2

iSee, 23.2.30

apf model, 23.8.12

icmPocketFinder, 23.5.10

atom charge, 23.4.21

insert column, 23.8.7

display, 23.2.17

installation, 23.1

autosave, 23.2.33

interactions, 23.2.12

backbone, 23.2.13

ligandbox, 23.5.9

background color, 23.2.2

measure distance ring, 23.8.16

job, 23.5.19

merge, 23.4.5

beep, 23.2.35

modeling, 23.7

binding energy, 23.5.2

molcart 64bit, 23.1.3

blend transition, 23.2.31

query, 23.9.5

breaks, 23.2.34

sdf, 23.9.4

change torsion, 23.4.16

text search, 23.9.6

chem table display, 23.8.4

molecule c, 23.2.5

chemical monitor, 23.8.10

moledit, 23.8.2

query2, 23.8.1

movie planes, 23.2.19

cheminformatics, 23.8

newscript, 23.10.1

clipping plane, 23.2.11

nmr, 23.4.18

closest, 23.4.22

nvidia error, 23.1.2

color carbon, 23.2.4

origin, 23.2.10

skin, 23.2.16

plist, 23.1.9

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, 5.5.12

scanScoreExternal2, 23.5.18

fixed torsion, 15

score, 23.5.8

flexibility, 5.6.5, 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 groups, 17.13

solvent accessible surface table, 23.4.19

ring sampling level, 12.2.1.3

ss, 23.4.17

flood, 9.22.17

structure, 23.4

fog, 3.6.3.5, 6, 6.10.1

superimpose, 23.4.6

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, 18.1.40, 18.7.4

surface display, 23.2.37

preferences, 4.20.7

thoroughness, 23.5.12

size, 8.7, 23.1.16, 23.2.1

transparent ribbon, 23.2.3

form view, 18.1.5

truncate mesh, 23.2.15

formal, 5.1.3, 23.4.21

view stack, 23.9.8

charge, 6.1.9, 10.15, 10.18

weak hydrogen bonds, 23.4.20

format, 18.1.2, 18.1.40

write pdb, 23.4.3

formula, 10.4.9, 10.11

faqcontour, 23.2.28

fragment, 10.3.35, 10.36.1, 13, 13.2, 17.11

faqhbondstrength, 23.2.29

linking, 17.11

faqmaps, 23.2.27

screening, 13.2

faqoda, 23.2.26

fragments, 10.8

faqstereo, 23.1.14

frame, 8.3.3

fasta, 8.1.5

free energy, 9.13, 9.14

fbdd, 13.2

radical, 10.4.7

fft, 12.13.1

wilson regression analysis, 10.36.2

protein protein docking, 12.13.1

freedomspace, 10.5.5

file, 3.6.1.3

freeze column, 18.1.30

close, 3.6.1.13

row, 18.1.31

compatible, 3.6.1.10

frequency, 10.3.35

export, 3.6.1.12

front, 6.3.10, 6.13.1

high quality image, 6.15.1

full model, 9.1.3

load, 3.6.1.7

builder, 9.1.3

menu, 3.6.1

multiple chain, 9.1.3.1

password, 3.6.1.11

refinement, 9.1.3

screen, 3.6.3.8

preferences, 4.20.4

function, 18.1.26, 18.1.32

tabs, 3.7

functional, 15

guided docking, 12.5, 23.5.3

groups, 10.13

h-bond, 5.2.4, 5.2.4.1, 5.2.4.2, 23.2.12

furanose ring conformation, 5.5.12

halogen, 10.11.2

fuzzy, 12.7

hardware stereo, 3.6.3.7, 23.1

gap, 9.4

hba, 13.1.10

general preferences, 4.20.5

hbd, 13.1.10

generalselecttools, 4.6.1

hbond, 5.2, 22.3.6, 23.2.29

generator, 5.3.3, 10.23

strength, 23.2.29

geometry optimization, 15

header, 4.2.7, 18.4.9

getting started, 4

health, 5.6.4

giga search, 10.5.5

heatmap, 18.4.7

sized library, 13.5

example, 18.4.7.1

gigasearch, 10.5.5

helix, 23.2.20

ginger, 10.23

help, 2

glasses, 6.6, 23.1.6, 23.1.14

videos, 2

global side-chain sampling, 9.19

hetero, 10.3.28

glutamine proline, 9.22.2

scan, 17.7

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, 18.1.39

gpcr_model, 22.5.1

column, 18.1.28

graft loop, 9.5

high, 3.6.1.15

graphical, 23.2.4

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, 22.1

his, 23.4.15

2D3D labels, 22.1.4

histidine, 9.22.2, 23.4.15

annotation, 22.1.2

tautomer, 23.4.15

color representation, 22.1.1

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

labels, 22.1.3

bins, 18.4.3

user interface, 23.2

options, 18.4.2

card, 23.1.2

bin.size, 18.4.2

controls, 6

bins, 18.4.3

defects, 23.1.12

color, 18.4.2

effects, 6.10

source, 18.4.2

panel, 6.2

style, 18.4.2

preferences, 4.20.3

title, 18.4.2

shadow, 3.6.3.13, 6.10.2

historeceptomics, 4.16.9

green arrows, 8.7.16, 23.6.2

hitlist, 12.4, 12.4.3, 13.1.8, 13.1.9.1, 13.1.9.5, 14.4, 23.5.7

lines, 8.2, 23.6.1

cluster apf, 13.1.9.5

grid, 10.3.3, 10.37, 22.12.1, 23.8.4

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, 17.6

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, 22.5

column, 18.1.46

model, 9.1, 9.1.1.2

groupGen, 17.18

introduction, 9.1.1

groups, 10.8, 10.11, 10.12

older versions, 9.1.1.3

guanidinium, 10.15

hover, 18.4.26

gui, 4.1, 4.20.4

3D editor, 22.7

menus, 3.6

add columns, 10.3.4

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, 5.2.4, 5.2.4.1, 5.2.4.2, 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, 5.2.4.1

filter, 10.3.12

move, 5.2.4.2

find replace, 10.3.13

bonds, 5.2.1, 12.1.5

mark row, 10.3.14

bond, 10.4.9, 23.4.20

markush, 22.6.8

hydrogens, 10.3.28

structure, 22.6.7

remove, 10.3.18

merge tables, 10.3.23

hyperlink, 7.6.1, 7.6.2, 18.1.40

properties, 10.3.19

hyrophobic, 10.38.1

reactions, 22.6.10

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

reorder, 10.28.3

icb, 4.18.2, 4.19, 23.2.30, 23.3.3

sdf, 10.3.9

icm, 23.3.3

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, 23.1.13

effects, 3.1.5

object, 5.1, 22.3.2

images, 3.1.7

script, 18.1.40

labels annotation, 3.1.6

icm-crash, 23.1.13

pro crystallographic tools, 3.2.6

icmFastAlignment, 8.4

get started, 3.2.1

icmPocketFinder, 5.6.7, 23.2.14, 23.5.10

graphics, 3.2.2

icmdb, 20

plots, 3.2.8

icmjs, 7.16

sequence analysis, 3.2.7

icmpocketfinder, 22.3.7

structure analysis, 3.2.3

id, 18.1.27

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, 18.4.21, 23.1.20

selections, 3.1.3

advanced, 6.15.3

superimpose, 3.1.8

distortion, 23.1.20

search, 4.16

preferences, 4.20.6

hrydrogen.bond, 23.2.29

problem, 23.1.20

quality, 3.6.3.11

jpg, 6.15

quick, 3.6.1.14, 6.15.2

means, 18.7.1

images, 6.15

kcc, 16.3.1, 16.5

impose, 12.6.2

keep carboxyls neutral, 12.2.1.3

in-a-window, 23.1.7

kernel regression, 16.3.1

inchi, 10.20.3

chemical, 10.4.10

increment, 18.1.27

keyboard mouse, 6.11

id, 18.1.27

keystokes in chem-edit, 10.4.10

index, 23.9.6

kmz, 3.7.6, 6.3.7

induced, 23.5.15

knime, 21

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

label, 4.20.7, 18.7.4, 23.2.17

insert, 7.6.4

atoms, 6.8.2

column, 18.1.26

color, 6.8.7

image, 7.6.3, 18.1.34

move, 6.8.4

table, 18.1.34

residues, 6.8.3

row, 18.1.33

sites, 6.8.6

script, 7.6.4

variables, 6.8.5

install, 1, 10.10.1, 20.1, 23.1.3, 23.1.4

2D, 3.7.3

installation, 23.1

3D, 3.7.3, 6.8.1

interaction, 5.5.3, 10.6, 23.2.12

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, 17.3.12, 23.5.2

drag, 3.6.3.16

interactive, 12.3.1, 22.2

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, 22.10

variables, 6.8.5, 23.2.18

internal hydrogen bonds, 12.1.5

labeling, 6.8.1

internet explorer, 23.3

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, 18.1.23

large chemical space, 22.6.4

invisible residue label, 23.1.12

font, 23.1.16

ionization, 9.12, 9.12.1

size, 23.1.9

iqr, 18.4.23

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, 18.6, 23.8.12

isotope, 10.4.3, 10.5.1

learning, 11

iupac, 10.2.7, 10.3.20

theory, 11.5

javascript, 7.16

least.squares, 18.4.16

job, 23.5.19

library, 10.35.4

join, 10.32

reaction, 22.6.10

ligand, 5.2.3, 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

likeness, 10.11, 23.8.9

aide, 12.10

line, 4.20.5, 18.7.4, 23.2.12

based screen, 10.38.3, 13.3

lineWidth, 4.20.3

best replace, 17.6

link, 8.3.9

binding, 9.16

structure to alignment, 22.4

code, 4.2.4, 4.16.6

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, 5.3.4, 5.3.6, 5.3.7, 8.1

conformational entropy, 10.27.1

example alignment, 8.3.14

strain, 10.27.2

nmr model, 4.2.5

environment, 9.19

pdb hyperlinks, 4.2.6

optimization, 9.19

protein structure, 5.1.1

pocket, 5.2.1, 23.4.11

sequence, 8.1

surface, 17.3.2

extract pdb, 8.1.3

receptor contacts, 17.3.12

from file, 8.1.4

display, 5.2

paste, 8.1.2

interaction, 10.6

swissprot, 8.1.1

strain, 17.3.10

libraries, 9.22.6

surface, 5.2.3

local, 23.2.24, 23.2.25

tether, 17.12

databases, 19

vicinity, 9.19

minimization, 9.19

ligand-based, 13, 13.3

database.browse, 19.2

ligand-induced RNA conformational changes, 5.5.12

edit, 19.3

convert, 9.22.1

query, 19.4

editor, 17, 17.1

row, 19.3

binding.re-dock ligand, 17.9

localpdb, 23.2.24

display, 17.3

localseq, 23.2.25

edit, 17.5

lock, 6.3.10, 6.13.1, 10.3.31

energy, 17.3

log, 18.4.6, 18.4.11

hydrogen.bond, 17.3

logD, 10.11.8

pocket, 17.3

logP, 10.4.9, 10.11

preferences, 17.2

logS, 10.4.9, 10.11

restraint, 17.12

logarithmic, 18.4.11

surface, 17.3

logout, 3.6.1.19

tether, 17.12

loop, 9.3, 9.5, 23.2.20

optimization, 22.11.3

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, 22.5.2

ligedit distance restraint, 17.12.2

tutorial, 22.5.2

tab, 3.7.5

modeling, 9.1.4.2, 9.6, 9.7, 9.22.10

tether, 17.12.1

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

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, 9.21

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, 5.3.4, 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

molt, 19.1

clip, 6.3.10

receptor maps, 12.2.1.2

color lighting, 6.3.9.4

selection, 4.6

options, 6.3.9

level, 4.6.3

representation, 6.3.9.3

bond, 23.4.2

save, 6.3.11

disulfide, 9.10, 23.4.17

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, 16.7

manual change torsion, 17.5.4

min, 18.7.1

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, 22.12.1, 23.2.27, 23.2.28, 23.5.9

global, 9.22.8

mark, 18.1.45

local, 9.22.8

row, 18.1.45

minimum specifications, 1

color, 18.4.14

mmff, 9.22.6, 10.4.16, 23.2.17, 23.8.5

shape, 18.4.13

type, 6.8.2

size, 18.4.13

mmp, 22.6.11

markush, 10.28.7, 10.35.1, 10.35.3, 10.36.1, 22.11.3

mnSolutions, 4.20.10

docking, 22.11.3

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, 22.5

library, 22.6.8

domain interaction, 9.18

mass, 23.4.22

start, 9.1.1.2

matched pair, 10.36.6, 22.6.11

weight, 11.1.4

analysis, 10.36.6

modelers view, 9.1.4.1

materials, 3.7.6

view, 9.1.4.1

max, 18.7.1

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, 17.5.6

mcs, 10.28.6, 10.30.1

modify, 9.12.2

rgroup decomposition, 10.28.7

amino acid, 9.12

mean, 18.4.6, 18.4.23, 23.4.7

group, 9.11

measure distance, 23.8.16

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

to ring, 23.8.16

mol2, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6

median, 18.4.6, 18.4.23

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

membrane, 12.1.7, 14.3

add database, 10.10.3

connect, 23.9.2

load models, 16.1.1

download dbs, 23.9.3

run, 16.1

hostid, 23.9.1

model type, 16.3

installation, 10.10.1

results, 16.2

license, 23.1.4

molskin, 6.3.2

search, 10.10.4

molsynth, 10.11.7

start, 10.10.2

molt, 19, 19.4

connect, 23.9.2

monitor, 23.8.10

hostid, 23.9.1

monochrome, 10.3.28

license, 23.9.1

montecarlo, 23.9.7

molclart, 23.1.4

mouse, 4.4, 6.11, 6.12

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

mov, 6.16, 6.16.2

animations slides, 7

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, 23.4.5

documents, 22.2

column, 18.1.28

dynamics, 14, 14.1, 14.2, 14.3, 14.4

mesh, 6.3.9.2

membrane, 14.3

slide, 7.4.2

restraints, 14.2

structure, 6.12

run, 14.1

tools, 6

vls, 14.4

rotate, 6.11

editor, 23.8.2

slab, 6.11

graphics, 6

translate, 6.11

matched pairs, 22.6.11

z-rotation, 6.11

mechanics, 9.22

zoom, 6.11

convert, 9.22.1

movie, 6.16.1, 23.2.19, 23.9.7

design loop, 9.22.10

montecarlo, 23.9.7

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, 22.6.11

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, 15

parameter optimization, 10.34

table, 10.20.2

template, 9.1.4.3

weight, 10.4.9

windows, 6.2

molecule, 23.2.8, 23.8.3

multiple, 12.6.2, 22.12.1

editor, 10.4

chain, 9.1.2.2, 9.1.3.1

moledit, 10.4.8

position group scan, 17.7

molmechanics, 23.9.8

rec, 12.6.2

minimize, 9.22.8

receptor, 4.16.1, 22.12

mmff, 9.22.6

docking, 17.15

molscreen, 13, 16

protein, 23.2.5

custom model panel, 16.4

mutant, 9.11, 23.4.13, 23.4.14

residue, 23.4.13

with password, 3.6.1.4

N C, 23.4.14

movie, 6.16, 6.16.2

mutation, 9.11, 9.13, 9.14, 9.16, 22.5.3, 22.5.4, 23.4.13, 23.4.14

password, 3.6.1.4, 4.18.1

protein binding, 9.13

optimal, 5.6.6, 12.13, 12.13.2, 12.13.3

ligand, 9.16

optimize, 9.22.2

peptide, 9.15

oracle, 20

stability, 9.14

orange, 4.6.5

mysql, 20

selection, 4.6.5

navigate workspace, 4.6.10

origin, 6.8.12, 23.2.10

nearest, 23.4.22

orthosteric, 5.6.7

nephrotox, 10.11.4

other selection, 4.6.19

neural network, 12.4.3.1, 17.18

outside, 23.5.9

Torsion Profile Neural Network Prediction Engine, 6.12.6.1

overlay, 22.3.3, 23.2.5, 23.4.6

new, 8.1

pH, 5.6.2, 10.19

icm session, 3.6.1.2

pKa, 5.6.2, 9.12, 9.12.1

table, 18.1.1

package.activeicm, 7.13

table, 18.1.1

packing, 5.3.1

nmr, 23.4.18

pages, 20.7

model, 4.2.5

pairwise, 10.37.5, 10.37.6

nnc, 16.3.5

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, 18.1.35

non-contiguous selection, 4.6.18

pca, 18.5

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, 22.3, 23.2.24, 23.2.25, 23.4.4

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, 23.4.3

geometry, 5.5.12

html, 4.2.7

puckering, 5.5.12

preparation, 22.3.11

number of sp3, 10.11.2

search, 4.2.3, 4.2.4, 22.3.1

numbers, 10.3.28

hyperlinks, 4.2.6

nvidia, 23.1.2

convert, 9.22.1

obj, 6.7

recent, 3.6.1.18

object, 4.12, 4.19, 22.3, 23.2.8

search, 3.7.4, 4.2, 4.2.1

objects, 5.1.2

pdbsearchfield, 3.6.2.13

in table, 18.3

pdbsearchhomology, 3.6.2.15

in.table, 18.3

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, 22.3.10

modeling, 9.21

oda, 5.6.6, 12.13, 12.13.2, 12.13.3

editor, 17.21

older version, 3.6.1.10

percentage similarity, 8.7.15, 22.4.4

omega, 6.8.5, 23.2.18

perspective, 3.6.3.9, 6.10.6

online databases, 10.5.5

ph4, 10.5.6

open, 3.6.1.3, 4.18, 18.1.2

draw 2d, 10.5.6.1

file, 4.18

3d, 10.5.6.2

password, 4.18.1

search, 10.5.6.3

2D, 22.6.6

logarithmic, 18.4.12

3D, 22.6.5

pls, 10.21, 10.22, 11, 18.6, 22.13

clone, 10.5.6.2

pmf, 23.5.6

draw2D, 10.5.6.1

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

draw3D, 10.5.6.2

pocket, 4.9, 5.2, 5.2.2, 5.2.3, 5.6.7, 22.3.7, 23.2.14, 23.4.11, 23.5.10

edit, 10.5.6.1, 10.5.6.2

conservation, 23.4.12

move, 10.5.6.2

properties, 5.8

new, 10.5.6.2

surface, 5.2.2, 13.1.11

search, 10.5.6, 10.5.6.3, 22.6.5, 22.6.6

peptide, 4.9

phase angle P, 5.5.12

properties, 4.9

phi, 6.8.5, 23.2.18

pocketome, 4.16, 4.16.1, 5.8

phylogenetic, 8.7.8

pockets, 5.6.7

phylogeny, 8.7.8

point label, 18.4.19

physics-based score, 12.4.3.1

portait, 4.20.6

pi, 5.2.5

post edit ligand, 17.5.8

cation, 5.2.5

screen, 13.1.9

pi, 5.2.5

postscript, 4.20.6

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, 18.4.8

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, 23.2.18

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, 23.2.11, 23.2.19, 23.2.21

ppsetreceptor, 12.13.5

faq, 23.2.21

ppt, 7.12, 7.14, 23.3.3

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

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

R group sar, 10.36.4

disulfide, 9.17

axis, 18.4.11

metabolic oxidation, 16.7

color, 18.4.14

predicting bioassays, 11.2

columns, 18.4.6

compound properties, 11.2

function, 3.6.9, 3.6.9.1

prediction binding, 9.13

grid, 18.4.15

preferences, 4.20, 13.1.5, 23.2.24, 23.2.25

header, 18.4.9

preferred residues, 9.6

inline, 18.4.22

presentation, 7.6.5, 7.7, 7.12

logarithmic, 18.4.12

presentations, 7

mark, 18.4.13

preserve, 23.8.6

mean median iqr, 18.4.23

press-and-hold to rotate, 10.4.8

point label, 18.4.19

pretty view, 17.3.6

preferences, 4.20.8

primary aliphatic amines, 10.15

groups, 18.4.25

principal component analysis, 18.5

regression, 18.4.16

regression, 11

selection, 18.4.18

components, 11.5

zoom translate, 18.4.17

print, 6.7, 18.4.20, 18.7.3

axis, 18.4.15

alignment, 8.7.4

display, 18.4.15

plot, 18.4.20

grid, 18.4.15

alignment, 8.7.4

inline, 18.4.22

printer.resolution, 4.20.6

probe, 12.2.1.1, 23.5.13

protein-ligand complex, 9.19

problem, 23.1.14

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, 22.10

with selection, 23.1.12

docking refinement, 12.13.11

prodrug, 10.26

protein-proteindocking, 12.13.7

profile, 4.16.9, 8.3.8

convert, 9.22.1

project, 3.6.1.5, 12.13.4, 20.6, 22.6.4.6

protonated, 23.4.15

close, 3.6.1.13

protonation, 9.12, 9.12.1, 10.19, 12.1.4

rename, 3.6.1.9

charge, 9.12.1

properties, 6.8.2, 10.11, 10.11.1, 23.8.7

state, 12.1.4

property, 10.4.9, 23.8.7, 23.8.8, 23.8.9, 23.8.10

states, 5.6.2, 9.12, 9.12.1

expression, 13.1.9.4

protonation_ph, 10.19

monitor, 10.4.9

protonation_ph_charge, 10.19.2

protac, 12.14

protonation_ph_concentration, 10.19.1

protect, 7.6.8

protprot, 12.13

protein, 5.4.6, 8, 9.15, 23.4.5

proximity, 6.3.3, 6.3.4

chain, 9.4

psa, 10.4.9, 10.11.9

health, 5.6.4

pseudorotation P, 5.5.12

model, 9.20

analysis, 5.5.12

preparation, 9.12, 9.12.1

phase angle, 5.5.12

protein docking, 22.10

psi, 6.8.5, 23.2.18

tutorial, 22.10

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, 17.9.1

analysis, 5.5

pyramid, 12.1.6

closed cavities, 5.5.4

pyramidal, 12.1.6

contact areas, 5.5.3

qm color by qm electrostatic potential, 15.6

distance, 5.5.6

introduction, 15.1

find related chains, 5.5.1

minimimize, 15.2

finding dihedral angle, 5.5.8

confromers, 15.3

planar angle, 5.5.7

set charges, 15.5

rama export, 5.5.10

torsion scan, 15.4

ramachandran plot, 5.5.9

hydrogen bond, 5.2.4

rmsd, 5.5.2

pdb chem gl, 5.1.3.2

surface area, 5.5.5

iw, 5.1.3.1

similarity, 5.7

qsar, 10.21, 10.22, 11.1, 22.13

tutorials, 22.3

learn predict, 10.21

analysis, 22.3.4

predict, 10.22

contact area, 22.3.5

quad buffer stereo, 23.1

convert, 22.3.2

buffer, 23.1.7

hydrogen bond, 22.3.6

quality, 3.6.1.15, 4.20.5

icmpocketfinder, 22.3.7

quantum chemistry, 15

search, 22.3.1

mechanics, 15

superimpose, 22.3.3

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

superposition, 5.4

molt, 19.4

select, 5.4.1

processing, 10.5.3

sites by apf, 5.4.6

setup, 10.5.1

superimpose 3D, 5.4.3

quick, 4.15

grid, 5.4.5

image, 6.15.2

multiple proteins, 5.4.4

model multiple chain, 9.1.2.2

start move structure, 4.4

side chain, 9.9

read pdb, 4.2

sidechains, 9.1.3

representation, 4.7

refinement, 12.6.4

what is selected, 4.6.4

region, 12.13.7

display.distance, 6.9.1

regression, 10.36.2, 11.1, 11.5, 18.4.16, 22.13

start color, 4.8

regul, 9.8

quit, 3.6.1.19

regularization, 9.8, 9.22.3

group, 10.28.7, 10.35.4

relationship, 11, 18.6

table, 10.35.2

covalent geometry, 12.2.1.3

groups, 10.35.2

relaxed ligand, 17.3.9

r-group, 10.28.7, 10.35.2

reload, 12.4.5, 23.5.4

decomposition, 10.28.7

dock results, 12.4.5

enumeration, 10.28.7

remove, 23.2.6, 23.2.7, 23.2.10

r-groups, 18.4.25

salt, 23.8.14

racemic, 10.3.28, 10.20.5, 23.5.21

explixit.hydrogens, 10.12

radar, 18.4.6

salt, 10.12

rainbow, 4.20.5, 6.8.16, 10.3.35, 23.2.38

rename, 18.1.25

ramachandran plot, 5.5, 5.5.10

column, 18.1.25

random forest, 11, 22.13

project, 3.6.1.9

range, 6.10.7.2

renumber, 9.2, 23.4.4

rapid isostere replacement, 13.4

reorder column, 18.1.29

ratio.selection, 4.20.5

replace chemical, 10.3.32

dock ligand, 17.9

replacement, 17.6

reactions, 10.8, 10.35.5

group, 17.8

reactive cysteine, 5.6.3

report, 20.3

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, 23.2.8, 23.4.15, 23.4.22

chemical, 10.1

alternative orientation, 22.3.11

spreadsheet, 10.3.1

content, 8.3.1

split, 11.1.1

names, 9.12, 9.12.1

table, 18.1.2

number selection, 23.2.36

pdb, 4.2, 4.2.1

pKa prediction, 5.6.2

table, 18

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, 23.4.13, 23.4.14

pdb codes, 3.6.1.18

residues, 5.2.2, 5.2.3, 23.2.14

receptor, 5.2.2, 5.2.3, 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

resize, 6.3.9.1, 6.15.3

considerations, 12.1.1

mesh, 6.3.9.1

flexibility, 17.15

resolution, 4.2.4

pocket, 17.3.1

restore, 3.6.2.11, 6.3.10, 6.13.1

surface, 17.3.1, 17.3.2

default, 23.1.9

refinement, 9.19

recent backup, 3.6.2.11

flexibility, 22.12.2

restrained docking, 12.5

recover, 3.6.2.11

restraint, 17.12.1, 17.12.2

cylinders, 8.7.16, 23.6.2

restraints, 14.2

lines, 8.2, 23.6.1

results, 12.13.10

redo, 3.6.2.10, 10.4.11, 17.5.5

stack, 12.4.2

refine, 9.8, 9.9

retrieve columns, 23.5.24

loops, 9.1.3

from original database, 23.5.24

rgroup, 10.35.4

molscreen, 16.1.2

ribbon, 3.7.1, 4.20.9, 6.1.3, 23.2.23, 23.2.34

rundock, 23.5.16

as a mesh object, 23.2.3

rxn, 10.4.13

faq, 23.2.23

safari, 23.3

preferences, 4.20.9

sali, 10.36.5

style, 4.20.9

bridge, 22.3.6

breaks, 6.1.3

salts, 10.3.18

cylinders, 6.1.3

sample, 9.20, 10.37

smooth, 6.1.3

double bond cis trans, 12.2.1.3

worm, 6.1.3

ligand pocket, 9.19

ribbonColorStyle, 4.20.9

peptide, 9.21, 9.22.12

ribose pseudorotation, 5.5.12

protein, 9.20, 9.22.11

pucker, 5.5.12

racemic centers, 12.2.1.3

ring, 5.5.12

sar, 10.28.7, 10.36, 18.4.25

conformation, 5.5.12

analysis, 10.36

torsion angles, 5.5.12

table, 10.36.3

ride, 13.4

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

gpu benchmark, 13.4.1.2

SMILES, 10.4.15

server setup, 13.4.1.1

alignment, 8.7.3

setup, 13.4.1

PDB, 4.19

ridge, 13.5

pdb, 4.19

right, 4.13

chemical mol, 10.4.13

click, 4.13

spreadsheet workspace, 10.2.1

rigid, 10.37

to chemical spreadsheet, 10.4.14

substructure superposition to template, 10.37.2

docked ligand, 17.20

ring, 5.2.5, 10.4.3, 10.4.6, 10.5.1

file, 4.19

stacking, 5.2.5

hits, 17.5.7

rings, 10.3.28, 10.23, 10.37

image plot, 18.4.21

rmsd, 5.5, 5.5.2, 23.4.7, 23.4.8

ligand receptor complex, 17.20

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, 23.4.7

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, 23.8.13

slide, 7.4

chemical, 10.3.34

smiles string, 10.4.15

torsion, 6.12.6.1

table, 18.1.21

when pasting, 10.4.8

spreadsheet, 17.5.7

easy, 3.6.3.12

tree, 18.7.3

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, 23.2.37

picture, 3.6.1.15

row, 18, 18.1.22, 18.1.35, 18.1.45

project, 3.6.1.8, 3.6.1.9, 3.6.1.10, 4.11

flag, 18.1.13

table.view, 18.1.8

height, 18.1.7, 23.2.39

saving, 3.6.1.8

mark, 18.1.13

project, 3.6.1.8

hide, 10.3.8

scaffold, 10.14

show, 10.3.8

hopping, 17.8

ruler, 6.8.16

scale, 4.20.5, 23.2.38

hits, 12.4.1

residue, 4.6.13, 4.6.18

group, 17.7

by number, 4.6.18

scan_pockets, 5.8

number, 4.6.18

scarab, 20

tree, 18.7.2

add user, 20.5

atom, 4.6.3

browse export data, 20.4

graphical, 4.6.3

installation, 20.1

object, 4.6.3

new project, 20.6

purple.box, 3.6.3.23

pages, 20.7

residue, 4.6.3

query, 20.3

workspace, 4.6.3

upload data, 20.2

selectall, 3.6.2.3

scare, 12.6.4

selecting.neighbors, 4.6.16

scatter, 13.1.9.2

selection, 4.6.4, 4.6.5, 4.6.21, 6.3.4, 10.4.11, 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

score, 12.4.3.1, 13.1.8, 17.4, 22.8.3, 22.8.5, 23.5.7, 23.5.8, 23.5.18

clear, 3.6.2.7

threshold, 13.1.4

neighbors, 3.6.2.8

screen, 10.38, 22.8.4, 22.9, 22.11.1

alignment, 4.6.19

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

all, 3.6.2.3

screenshot, 6.16, 6.16.2

alter, 4.6.7

movie, 6.16.2

atom, 3.6.2.5

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

basic, 4.6.2

sculpting, 9.18

change, 4.6.7

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, 17.10, 19.1, 20.2, 22.11.2, 23.9.3, 23.9.4

clear, 3.6.2.7

search, 5.7, 10.10, 10.10.4, 19.2, 20.3, 23.9.6

column, 18.1.23

chembl, 4.16.2

filter, 3.6.2.5, 4.6.8

drugbank, 4.16.7

graphical, 4.6.16

filter, 10.5.2

invert, 3.6.2.6, 18.1.23

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, 18.1.23

sequence, 4.2.3

residue, 3.6.2.5

tautomer, 10.5.3

row, 18.1.23

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, 23.2.20

table, 4.6.19, 18.1.23

structure, 3.6.4, 6.1.3, 8.3, 8.3.2

elements, 18.1.23

select, 4.6.12, 4.6.13, 18, 18.1.45, 23.4.22

tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8

a tree branch, 18.7.2

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, 22.3, 22.4, 22.4.4, 23.4.12, 23.6, 23.6.1

editor, 8.5

error, 23.1.19

identity, 8.7.15

stereo, 3.6.3.6

pattern, 4.2.3

chain refinement, 17.14

reordering, 8.7.8

chains, 9.9

secondary structure, 8.2, 23.6.1

side-by-side, 23.1.19

similarity, 8.7.15

side-chain optimization, 9.19

sites, 8.5

sampling, 12.13.11

structure, 8.3.6

side-chains, 12.6.1

type, 8.3.4

sigmaLevel, 5.3.6, 5.3.7

DNA, 8.3.4

similarity, 10.31

alignment, 8.3.5, 8.6.2, 8.6.6

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

amino acid, 8.3.4

length, 23.5.12

nucleotide, 8.3.4

simulations, 23.7

protein, 8.3.4

single, 10.4.10

search, 8.4

chain, 9.1.2.1

structure.alignment, 8.3.6, 8.6.3

single-point energy, 15

sequences, 8, 23.2.25

singlet, 10.4.7

unique, 8.3.13

sites, 5.4.6

extract, 8.3.13

size, 5.2.4.1

unique, 8.3.13

sketch accents, 6.10.3

server, 13.1.7.2

markush, 10.35.1

error, 23.1.17

reaction, 12.8.1

set, 10.3.31, 23.4.21

smiles, 10.4.12

formal charges, 10.15

accents, 3.6.3.14, 6.10.3

server, 23.1.17

skin, 3.7.1, 6.1.4, 23.2.16

bond type, 9.22.5

slab, 6.3.10, 6.13.1

charges, 9.22.6

slice, 6.13

chirality, 9.22.5

slide, 6.10.7.4, 7.2, 7.3.1, 7.6.1, 23.2.31

disulfide, 9.10, 23.4.17

effects, 7.5

bond, 9.22.5

movie, 6.16.1

formal charge, 9.22.5

file, 7.2

tether, 9.22.5

navigation, 7.3.2

types, 9.22.6

show, 7.3

setAPFparams, 23.8.12

blend, 7.5

setup, 12.13.6

edit, 7.4.1

ligand receptor, 17.1

effect, 7.5

shade, 8.7.7, 8.7.7.1

smooth, 7.5

alignment, 22.4.4

transition, 7.5

shading, 6.3.12

slides, 6.16.1, 7, 7.1, 7.3, 23.2.30

shadow, 6.10.2

smiles, 10.4.9, 10.11, 10.20, 10.20.3, 10.20.4

share model, 11.1.5

smooth, 6.3.9.3

sheet, 23.2.20

surface, 23.2.37

shell preferences, 4.20.10

solid, 6.3.9.3

shift, 6.8.3

solvent.accessible.area, 23.4.19

shine, 3.7.2, 4.20.5

sort hitlist, 13.1.9.1

shineStyle, 4.20.3

table, 3.6.10.4

show, 7.3.1, 18.1.39

sorting, 13.1.9.1

hide column, 18.1.39

compounds, 18.7

side, 10.3.29

sp3, 10.11.2

by side, 10.3.29

spec, 3.7.2

specs, 1

ring puckering, 5.5.12

faq, 23.1.5

sulfur, 9.10

speed, 6.10.7.2

superimpose, 3.6.8, 5.4.2, 5.4.6, 10.37.4, 22.3.3, 23.2.5, 23.4.6, 23.4.7, 23.4.8

sphere, 23.4.11

3D, 5.4.3

spherical, 23.4.9, 23.4.12

Calpha, 5.4.3

split, 10.36.1

arrange.grid, 5.4.5

spreadsheet, 10.20.2

backbone, 5.4.3

square, 23.4.7

heavy atoms, 5.4.3

stability, 9.14, 22.5.3, 22.5.4

multiple, 5.4.4

stack, 9.20, 9.22.18, 12.4, 12.13.10, 23.9.8

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

calculations, 9.22.18

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

stacking, 5.2.5

area, 5.5

standalone hitlist, 12.4.4

area, 5.5.5

standard table, 18.1

surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5

standardize, 10.12

surrounding, 23.4.11

table, 10.12

swissprot, 8.1, 8.5

start, 10.10.2

sxstrace, 23.1.19

startup, 23.10.2

symmetric oligomer, 9.1.3

static, 23.4.8

symmetry, 5.3.1, 5.3.3, 22.3.8, 22.3.9

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

synthesize, 10.11.7

bond, 10.4.2

synthetic feasibility, 10.11.7

hardware, 3.6.3.7

system preferences, 4.20.11

side-by-side, 3.6.3.6

tab, 18.1.2, 18.1.21

stereohard faq, 23.1.6

pdb, 3.7.4

stereoisomer, 10.20.5

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

stereoisomers, 10.25

alignment, 18.1.12

stick, 4.20.5

clone, 18.1.16

stl, 6.7

color, 18.1.10

stop, 6.10.7.3

column format, 18.1.40

store, 3.6.3.19, 6.10.7.4, 23.2.22

copy, 18.1.36, 18.1.37

current view, 3.6.3.19

delete, 18.1.17

faq, 23.2.22

edit, 18.1.24

strain, 5.6.4, 6.12.6.1, 10.17, 10.27, 10.27.2, 12.1.10, 12.4.3.1, 17.4

filter, 18.1.43

strip, 23.4.9

find, 18.1.9

structure, 5.3.3, 11, 18.6, 22.3, 23.4

replace, 10.3.32

analysis, 5.5.12, 22.3.4

font, 18.1.11

ensemble, 9.22.14

size, 23.2.1

preparation, 9.19

grid, 18.1.5

representation, 6.1

histogram, 18.4.1

smiles, 10.20.4

insert, 18.1.26

structure-based, 13

layout, 18.1.5

structures, 10, 10.1

learning, 18.6

style, 4.20.5

mark, 18.1.13

substituent, 10.9.1, 10.9.2, 10.35.2, 17.5.2

row, 18.1.13

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

mouse, 18.1.47

template, 17.12.3

navigation, 18.1.4

alerts, 10.13

new column, 18.1.26

sugar conformation, 5.5.12

plot, 18.4

pucker analysis, 5.5.12

print, 18.1.19

puckering, 5.5.12

rename, 18.1.15

row height, 23.2.39

row, 18.1.33

save, 18.1.3

rows, 3.6.10.7

selection, 18.1.3

save, 10.3.9, 18.1.3, 18.1.4, 18.1.21

search, 18.1.9

scale, 18.1.18

select, 18.1.23

scroll, 18.1.4

setup, 18.1.18

sdf, 10.3.9

sort, 18.1.42

select, 18.1.23

split fragments, 10.3.33

setup, 18.1.18

view, 18.1.5

sort, 3.6.10.4, 10.3.5, 18.1.42

save, 18.1.8

standard, 18.1

zoom translate, 10.3.30

view, 10.3.29

action, 18.1.47

width, 18.1.4

alignment, 18.1.12

tables, 10.31, 18

append, 18.1.43

tag, 4.6.21, 17.5.7, 18.1.46

clone, 18.1.16

tags, 4.6.21

color, 18.1.10

m, 5.5.12

column, 10.3.4, 18.1.26, 18.1.32, 18.1.39

tautomer, 10.24, 23.4.15

columns, 10.3.8

tautomers, 10.24

compare, 10.3.22

temperature, 5.6.5

copy, 10.3.6

template, 9.1.2, 10.4.6, 10.37

cursor, 18.1.47

docking, 23.5.3

delete, 18.1.14, 18.1.17

templates, 10.4.6

display, 23.10.4

terminal, 10.3.28

double.click, 18.1.47

font size, 23.2.1

edit, 10.3.17

tether, 12.5, 17.12.1, 17.12.2

excel, 10.3.10, 18.1.20

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

filter, 10.3.12, 18.1.43

search, 10.5.4

find-replace, 10.3.13

texture, 3.7.6

to screen, 18.1.4

thoroughness, 10.23, 10.37, 23.5.12

font, 18.1.11

three, 10.3.24, 23.8.6

foreground, 23.10.4

threshold, 4.20.5

grid lines, 18.1.4

tier, 4.14

hide, 18.1.39

time, 23.5.11

hyperlink, 10.3.15

machine, 23.1.15

insert, 18.1.33

tissue, 4.16.9

join, 3.6.10.5

racemic, 10.20

label, 10.3.14

tools 3D, 3.6.6

landscape, 18.1.18

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, 18.1.47

plot function, 3.6.9.1

name, 18.1.15

superimpose, 3.6.8

new, 18.1.1

table, 3.6.10

options, 18.1.14

Learn, 3.6.10.1

orientation, 18.1.18

clustering, 3.6.10.3

portrait, 18.1.18

merge, 3.6.10.5

print, 10.3.11, 18.1.4, 18.1.19

predict, 3.6.10.2

read, 18.1.2

tooltip, 18.4.26

rename, 18.1.15

balloons, 18.4.26

right click, 18.1.14

torsion, 6.12.6, 6.12.6.1, 9.22.7, 10.17, 17.5.4, 23.4.16

angles, 6.12, 6.12.6

undisplay-all, 3.6.3.1

free strain, 10.17

origin, 6.8.12

scan, 9.22.7, 15

undo, 3.6.2.9, 4.20, 10.4.11, 17.5.5

toxscore, 10.11.3

redo, 17.5.5

trace, 6.1.10

uniprot, 4.16.5, 8.5

transition.blend, 23.2.31

unique, 10.3.28, 10.33

transitions, 7, 23.2.30

unit, 5.3.3

translate, 4.4, 6, 6.12, 10.3.30

units, 23.5.1

translation, 6.12.3, 8.3.3, 18.4.17

unix, 23.10.2

transparent, 6.3.9.3

unsatisfied hydrogen bonds, 17.3.8

background, 6.15.3

unusual peptide, 4.17

ribbon, 23.2.3

upload, 20.2

surface, 23.2.37

use activeicm, 7.12

tree, 8.7.8, 10.28.7, 18.7.2, 18.7.3, 18.7.4

user, 10.10.5, 20.5

branch swapping, 8.7.8

defined groups, 17.5.3

distance, 10.28.3

modifiers, 17.5.3

edit, 10.28.4

user-defined groups, 10.4.5

reorder, 10.28.3

van der waal, 6.8.15

triplet, 10.4.7

variable, 4.20.7, 23.2.8

trouble shooting, 23.1.11

verbose, 10.23

trouble-shooting, 23.1.12

large sdf files, 10.1.2

truncating a mesh object, 23.2.15

vicinity, 10.23

crash qlock, 23.1.13

video, 2, 6.16, 6.16.1, 6.16.2

tsv, 18.1.21

view, 3.6.3.19, 7.3.1, 10.3.28, 23.2.22, 23.9.8

tut analyze alternative orientations, 22.3.11

animate view, 3.6.3.15

occupancy, 22.3.10

center, 3.6.3.20

symmetry, 22.3.9

color background, 3.6.3.18

multiple receptor, 22.12.1

dock results, 12.4

tut3, 22.5

fog, 3.6.3.5

tut3e, 22.3.12

macroshape, 3.6.3.22

tut5a, 22.9.1

menu, 3.6.3

tut5b, 22.9.2

mesh clip, 6.13.1

tut5c, 22.11.1

perspective, 3.6.3.9

tut5e, 22.11.2

selection level, 3.6.3.3

tutorial 2D pharmacophore, 22.6.6

mode, 3.6.3.4

3D pharmacophore, 22.6.5

shadow, 3.6.3.13

chemical clustering, 22.6.3

sketch accents, 3.6.3.14

search, 22.6.2

slide show, 7.3.1

molecular documents, 22.2

tools, 3.6.3

sequence alignment, 22.4

tree, 18.7.4

link, 22.4.2

undisplay all, 3.6.3.1

load sequence, 22.4.1

stach, 9.22.15

sequence conservation, 22.4.3

virtual, 13.1, 13.1.1, 13.1.2, 22.9, 22.11.1

tutorials, 22

ligand screening, 16

two, 10.3.24, 23.8.6

screen, 13.3, 13.4

ubuntu, 23.1.18

screening, 13, 13.2

ultra large library, 13.5

examples, 22.11

unclip, 6.3.10, 6.13.1

virus, 5.3.3

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

ligand strain, 17.3.10

xstick, 6.1.2, 23.2.21

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

xyz, 23.2.10

analysis, 13.1.9.4

youtube, 2

display, 13.1.9.3

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

command line, 13.1.7.2

τm, 5.5.12

getting started, 13.1.2

histogram scatter plot, 13.1.9.2

introduction, 13.1.1

preferences, 13.1.4

results, 13.1.8

run, 13.1.6

score, 12.1.9

visualization, 13.1.11

results, 13.1.8

volume, 10.4.9

water, 9.22.17, 12.1.8

waters, 9.22.17

wavefront, 3.7.6, 6.3.11, 6.7

weak, 23.4.20

web, 22.2

browser, 3.6.1.12

weight, 10.11, 23.8.7, 23.8.10

weighted, 18.7.1

width, 18.1.22

window, 4.14

windows, 4.14.1, 10.10.1

wire, 3.7.1, 4.20.5, 6.1.1, 23.2.4, 23.2.21

wireBondSeparation, 4.20.1

working directory, 23.5.23

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, 18.4.21, 23.9.4, 23.9.7

alignment, 8.7.3

excel, 10.2.3

image, 3.6.1.15, 23.1.20

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, 18.1.3

writing a pdb file, 23.4.3

ray, 3.6.5

xi, 6.8.5, 23.2.18

xls, 10.2.3

xlsx, 10.2.3

xml, 20.2