ICM User's Guide: Index

modify group, 9.13.2

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, 18.21

Chemical Label, 6.8.11

Altona-Sundaralingam pseudorotation, 5.6.12

Interaction Diagram, 18.3.7

Area, 9.23.18, 24.2.26

bioisostere, 10.9.1

Atom Single Style, 4.20.3

chemical label, 6.8.11

Atomic Property Fields, 11.4, 23.14

from PDB, 10.1.1

B-factor, 9.8.3

interaction diagram, 10.6

B3LYP, 16

screening, 17

Bad Groups, 24.8.7, 24.8.10

to 3D, 10.20, 10.20.3

Baell, 10.4.9

depiction, 10.20.2

Beep, 4.20.11

3D, 6.6, 6.8.8, 10.1.3, 10.3.24, 10.3.28, 10.3.31, 10.20.2, 23.2

Beta-Catenin, 18.21

QSAR, 10.38.4, 11.4, 23.14

Bioactive Conformation, 18.21

chemical, 10.4.16, 10.20.1

Blast, 24.2.25

interactive ligand editor, 3.7.5

BlastDB Directory, 4.20.2

ligand editor, 18.3.4

alphas, 6.8.3

object, 6.3.9

C-alpha backbone, 5.6.11

pharmacophore, 13.1, 18.3.11

C2′-endo pucker, 5.6.12

print, 6.7

C3′-endo pucker, 5.6.12

printing, 6.7

CHEMRIYA, 12.6

screening, 17

COLLADA, 3.6.1.7

stereo, 6.6

CPK, 3.7.1

visualization, 5.6.11

CPU, 9.8.6

3DMOLT, 20.5

CYM, 9.13, 9.13.1

3DQsar, 11.4

CYS, 9.13, 9.13.1

3D_Similarity_PDB_Search, 5.8

ChEMBL, 4.16.2, 10.1

3Dqsar tutorial, 23.14

Chemical Cluster, 23.6.3

3d, 5.3, 5.3.1

Search, 23.6.2

bioisostere, 10.9.2

Chiral_Good, 9.8.7.2

predict, 5.7

CisTransAmide Angle, 12.7.7.4

helices strands, 5.7.1

Clash Threshold, 4.20.10

local flexibility, 5.7.5

Computational Chemistry, 18.21

protein health, 5.7.4

Computer-Aided Drug Discovery (CADD), 18.21

tools identify ligand binding pocket, 5.7.7

Covalent Geometry., 18.21

oda, 5.7.6

DFT, 16

4D, 12.9.2, 23.12.1

DILI, 10.11.5

dock, 18.15

DNA, 4.17, 8, 8.3.3

docking, 4.16.1

Decomposition, 10.36.3

6-31G*, 16

Design Evolution, 12.14

64, 24.1.3

Dimer, 5.6.11

A-form RNA, 5.6.12

Display, 24.2.26

AI, 12.14

Distance, 12.7.7.4

APF, 10.37.4, 10.37.7, 10.38.4, 11.4, 13, 17, 17.6, 23.14

Dock Directory, 4.20.2

template, 10.37.3

Docking, 24.2.26

ARG, 9.13, 9.13.1

Drug Bank, 4.16.7

ARN, 9.13, 9.13.1

Design, 18.21

ASP, 9.13, 9.13.1

Editor, 4.20.2

ASPH, 9.13, 9.13.1

Eintl, 12.1.10

Acetyl Cap, 18.21

Error in saving configuration settings: You are not a license administrator, 24.1.10

ActiveICM, 3.6.1.12

Extended Amino Acids, 18.21

gz, 4.20.2

hydrogenDisplay, 4.20.1

uue, 4.20.2

light, 4.20.3

FTP.createFile, 4.20.11

lightPosition, 4.20.3

keep File, 4.20.11

mapLineWidth, 4.20.3

proxy, 4.20.11

occupancy Radius Ratio, 4.20.3

Filter.zip, 4.20.2

occupancyDisplay, 4.20.3

Flexible Minimization, 18.21

quality, 4.20.3

Force Auto Bond Typing, 4.20.11

rainbow Bar Style, 4.20.4

Formula, 24.8.7, 24.8.10

resLabelDrag, 4.20.7

Free Wilson, 10.36.2

resize Keep Scale, 4.20.3

Frequently Asked Questions, 24

ribbonRatio, 4.20.9

GAMESS, 9.23.16

ribbonWidth, 4.20.9

GIF, 3.6.1.15, 6.16, 6.16.2

ribbonWorm, 4.20.9

GINGER, 10.23

rocking, 4.20.4

GLU, 9.13, 9.13.1

Range, 4.20.4

GLUH, 9.13, 9.13.1

Speed, 4.20.4

GPCR Modeling Example, 23.5.1

selectionStyle, 4.20.3

GPU, 9.8.6

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, 24.2.33

fontColor, 4.20.7

autoSaveInterval, 24.2.33

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, 20.5

HBA, 12.7.7.7, 24.8.7, 24.8.10

ISIS, 24.8.3

HBD, 12.7.7.7, 24.8.7, 24.8.10

Icm Prompt, 4.20.10

HF, 16

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, 18.3.7

HIP, 9.13, 9.13.1

Interactive Ligand Editor, 18.21

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, 16

KMZ, 3.6.1.7

Hbond to selection, 12.7.7.4

LBDdock, 9.8.7, 9.8.7.3

Hbonds, 18.3.4

LCC, 12.6

Helicon Peptide, 18.21

LYN, 9.13, 9.13.1

Homodimer, 5.6.11

LYS, 9.13, 9.13.1

Homologous chains, 5.6.11

LigStrain, 18.21

To Guide, 3

Ligand Strain, 18.21

Html, 4.2.7

Liver Toxicity Models, 10.11.5

Http Read Style, 4.20.11

Log Directory, 4.20.2

Hydrocarbon Staples, 18.21

LogP, 11, 19.6

Hydrogen.bond, 4.20.5

LogS, 11, 19.6

I+4 Staple Position, 18.21

MD, 15, 15.1, 15.2, 15.3, 15.4, 15.5

Staple Position, 18.21

Q and A, 15.5

ICM, 16

MOL, 10, 10.3.3, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 12.5.3, 19.2

Browser How To, 3.1

MOL2, 12.5.3

Pro How To, 3.2

MOLT, 20.1

analysis tools, 5.6.12

MOVIE.frame Grab Mode, 4.20.4

graphics crash, 24.1.11

MPO, 10.34

object, 5.7.2, 9.20

Mac, 24.1.15

start, 1

Atom Margin, 4.20.10

ICM-Pro Tutorial, 18.21

Sigma Level, 4.20.10

IMAGE.bondLength2D, 4.20.6

Markush, 23.6.9

color, 4.20.6

create, 23.6.7

compress, 4.20.6

File Size Mb, 4.20.11

gammaCorrection, 4.20.6

Max_Fused_Rings, 10.11

generateAlpha, 4.20.6

Mnconf, 4.20.10

lineWidth, 4.20.6

Model, 11.4

lineWidth2D, 4.20.6

Modify Amino Acid, 9.13

orientation, 4.20.6

Table, 9.8.7.1

paper Size, 4.20.6

MolCart, 24.9

previewResolution, 4.20.6

MolIPSA, 24.8.7, 24.8.10

previewer, 4.20.6

MolLogP, 24.8.7, 24.8.10

print, 4.20.6

MolLogS, 24.8.7, 24.8.10

printerDPI, 4.20.6

MolPSA, 10.11

scale, 4.20.6

MolScreen, 17

stereoAngle, 4.20.6

MolSoft ICM-Pro, 18.21

stereoBase, 4.20.6

MolVol, 10.11

stereoText, 4.20.6

Molcart, 10.5.3

INCHI, 10.20.3

MoldHf, 10.11, 24.8.7, 24.8.10

IQR, 19.4.6

Molecular Docking, 18.21

Preparation, 18.21

paper Size, 4.20.8

Movie.fade Nof Frames, 4.20.4

previewer, 4.20.8

quality, 4.20.4

rainbowStyle, 4.20.8

Auto, 4.20.4

seriesLabels, 4.20.8

Multimer, 5.6.11

PLS, 11.1

NCBI, 24.2.25

PNG, 3.6.1.15, 4.15, 6.16, 6.16.2

NH2 Cap, 18.21

PROPKA, 5.7.2

NVIDIA, 24.1

PROTAC, 14, 14.3

Natural Amino Acids, 18.21

PSA, 10.11.9

NephroTox, 10.11.4

Passaro, 9.8.8

Nof_Atoms, 10.11

Peptide Engineering, 18.21

Nof_Chirals, 10.11

Mode, 18.21

Nof_HBA, 10.11

Modeling, 18.21

Nof_HBD, 10.11

Stapling, 18.21

Nof_Rings, 10.11

Pharmacophore RMSD, 12.7.7.4

Nof_RotBonds, 10.11

PowerPoint, 23.2, 24.3

Non-overlap, 12.7.7.4

Projects Directory, 4.20.2

North conformation, 5.6.12

Prosite Dat, 4.20.2

Number of Conf, 9.8.7.1

Protein, 24.2.26

Nvidia GL failutre, 24.1.11

complex, 5.6.11

ODA, 24.2.26

Protein-Peptide Interactions, 18.21

Optimal, 24.2.26

Viewer, 4.20.2

Output Directory, 4.20.2

Pseudorotation Interactive Plot, 5.6.12

PAINS, 10.4.9, 10.11.3

Psi4, 16

chemicals, 10.4.9

Pub Chem, 4.16.8

PCA, 11.1, 11.5, 23.6.4

PubMed Reference, 19.1.40

analysis, 10.29

Pubchem, 4.16.8

PDB, 4.2.7, 5.1.2, 5.4.3, 5.8, 8.1, 10.1.1, 18.20

QSAR, 11, 11.1, 19.6, 23.14

7UWI, 18.21

R, 10.8, 10.36.1

Directory, 4.20.2

and S, 24.5.21

Style, 4.20.2

R-Group, 10.36.3

link, 19.1.40

R-groups, 18.5.3

Search, 3.6.2.12, 3.6.2.13, 3.6.2.14, 3.6.2.15, 3.6.2.16

REAL, 10.5.5, 12.6

Field, 3.6.2.13

RESP charges, 16

Homology, 3.6.2.15

RIDE, 13, 20.5

Identity, 3.6.2.14

RIDGE, 20.5

Sequence, 3.6.2.16

- Rapid Docking GPU Engine, 12.6

convert, 5.1.2

RMSD, 5.5.2, 9.23.18

PFAM, 3.6.1.7

RMSF, 9.23.18

PLOT.Yratio, 4.20.8

RNA, 4.17

color, 4.20.8

backbone conformation, 5.6.12

date, 4.20.8

chain analysis, 5.6.12

draw Tics, 4.20.8

conformation, 5.6.12

font, 4.20.8

pucker, 5.6.12

fontSize, 4.20.8

structure analysis, 5.6.12

labelFont, 4.20.8

sugar conformation, 5.6.12

lineWidth, 4.20.8

RTCNN, 9.8.7.2, 12.1.9, 12.7.1.2

logo, 4.20.8

Score, 18.21

markSize, 4.20.8

RTCNNorig, 9.8.7.2

orientation, 4.20.8

Ramachandran Plot, 5.6.9

Reinforce Helix Tool, 18.21

Uniprot, 19.1.40

Relax Geometry Command, 18.21

VHL, 14.3

Label Shift, 4.20.7

VLS, 12.5, 12.5.1, 12.5.2, 12.7.7.2

Style, 4.20.7

preferences, 12.5.4

Residue Replacement, 18.21

Van Drie, 10.36.5

RotB, 24.8.7, 24.8.10

Label Style, 4.20.7

Rotation angle, 5.6.11

Volume, 24.8.7, 24.8.10

Rotational symmetry axis, 5.6.11

Change, 12.7.7.4

Run Affinity Model, 9.8.4

Water Radius, 4.20.10

SALI, 10.36.5, 23.6.11

Wilson, 10.36.2

SAR, 11, 17.6, 19.4.25, 19.6

Wire Style, 4.20.1

table, 10.36.3, 23.6.9

Working with the Hitlist, 12.7.1.3

SCARE, 12.9.4

XPDB Directory, 4.20.2

SCORE, 24.5.6, 24.5.17

Xstick, 3.7.1

SDF, 10, 10.3.24, 10.3.25, 10.3.26, 10.3.27, 12.5.3, 19.2

_AFFINITY_PRED, 9.8.4

SEQUENCE.site Colors, 4.20.4

a-bright, 3.7.2

SITE.label Style, 4.20.7

about model, 11.1.3

labelOffset, 4.20.7

acceleration, 9.8.6

wrap Comment, 4.20.7

acceptor, 10.4.9, 10.38.1

SLIDE.ignore Background Color, 4.20.4

active, 7.7, 24.3.3

Fog, 4.20.4

activeICM, 7.8

SMILES, 10.1.2, 10.2.4, 10.4.12

activeicm, 7.7, 7.12, 7.14, 7.14.1, 24.3

Score, 12.1.9

advanced, 7.14

Select Min Grad, 4.20.10

background images, 7.15

Sequence Editing, 18.21

control, 7.13

Show Res Code In Selection, 4.20.7

activeicmjs, 7.16

Sidechain Optimization, 18.21

activity, 11, 19.6

Smiles, 24.8.7, 24.8.10, 24.8.11

cliff, 10.36.5, 10.36.6, 23.6.11

South conformation, 5.6.12

tutorial, 23.6.11

Special Cases, 10.34.1.1

add database, 10.10.3

Structural alignment, 5.6.11

new data, 10.3.7

Subunits, 5.6.11

to table, 18.5.7

SureChEMBL, 4.16.3

adding fragment, 10.4.8

Swissprot, 3.6.1.7

in editor, 10.4.8

Dat, 4.20.2

adjust row height, 24.2.39

link, 19.1.40

administration, 10.10.5

Symmetry, 5.6.11

advanced alignment selection, 8.7.14

TYM, 9.13, 9.13.1

affinity, 9.8.4

TYR, 9.13, 9.13.1

ai, 18.18

Temp Directory, 4.20.2

decoration, 18.18

Terminal Capping, 18.21

alanine, 12.9.4

Tools Analysis, 5.6.12

album, 6.15.3

Torsion Minimization, 18.21

alias, 10.4.5

Trimer, 5.6.11

align, 4.12, 10.14

USER.email, 4.20.11

color 2D scaffold, 10.14

friends, 4.20.11

dna protein, 8.6.4

full Name, 4.20.11

multiple, 8.6.5

organization, 4.20.11

sequence structure, 8.6.3

phone, 4.20.11

two sequences, 8.6.2

Ultra Large Libraries, 20.5

DNA to protein, 8.6.4

two sequences, 8.3.5, 8.6.2

acids, 9.13.1, 10.4.6

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, 23.4.4, 24.4.12, 24.6, 24.6.2

anaglyph, 6.6, 24.1, 24.1.8

annotation tutorial, 23.4.4

stereo faq, 24.1.8

box shade font, 8.7.7

analysis, 3.6.4, 8.3

editing, 8.7.1

charge states amino acids, 9.13

editor, 8.7

angle, 5.6.7, 5.6.8, 6.8.5, 6.9, 6.12.6, 10.16, 24.2.18, 24.4.16

example, 8.3.14

angstrom, 24.4.7

font size, 24.2.1

animate, 3.6.3.15, 6.10.7

format, 8.7.11

view, 6.10.7

gaps, 8.7.11

animation, 6.10.7.1, 6.10.7.2, 6.10.7.3, 6.10.7.4, 9.8.2.1

image, 8.7.2

store, 6.10.7.4

profile, 23.4.4

animations, 7

reorder, 8.3.12

annotate, 4.6.21, 10.13

search, 8.7.12

alignment, 8.7.6

secondary, 23.4.4

by substructure, 10.13

structure, 8.7.16, 24.6.2

plot, 19.4.24

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, 12.4, 12.7.7.5, 12.10, 13.1, 13.2, 18.3.11, 18.17, 23.8, 23.8.1, 23.8.2, 23.8.3, 23.8.4, 23.8.5, 24.8.12

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, 18.12.3

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, 23.8

options, 8.7.10

cluster, 23.8.5

rename, 8.7.10

consensus, 23.8.2

reorder, 8.3.12

score, 23.8.3

ruler, 8.7.10

screen, 23.8.4

save, 8.7.2

superposition, 23.8.1

search, 8.7.12

alignment, 10.37.7

selection, 8.7.13, 8.7.14

apf3Dqsa, 24.8.12

sequence offset, 8.7.10

apo, 12.7.7.7

table, 8.7.10

append, 19.1.44

view, 8.7.10

table, 19.1.44

alignments, 8.6, 23.4

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, 14.2, 14.2.2, 14.2.3, 23.3.5

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, 24.2.8

amidinium, 10.15

as2_graph, 4.6.5

amino acid, 4.17, 9.13

as_graph, 24.2.8

assign, 6.1.3

run, 12.3.3

2D coordinates, 10.20.2

bayesian classifier, 11

helices, 5.7.1

bbb, 10.11.6

strands, 5.7.1

beep, 24.2.35

atom, 4.20.5, 10.3.28, 24.2.4, 24.2.5, 24.2.8, 24.2.16, 24.2.17, 24.4.10

begin docking simulation, 12.3

charge, 24.4.21

best, 10.3.34

atomLabelStyle, 4.20.7

bicyclics, 10.4.6

atomic energy circles, 18.3.5

binding, 23.5.3, 24.2.14, 24.5.2, 24.5.10

partial charges, 16

free energy, 9.8.4

property field, 10.37.5, 10.37.6, 18.3.11

pocket, 9.20

score, 10.38.2

properties, 6.3.1

fields, 5.5.6, 5.9, 10.38, 10.38.1, 10.38.3, 12.4, 23.8

bioinfo align multiple, 8.3.7

attachment, 10.4.3, 10.5.1

two sequences, 8.3.5

point, 10.35.4

links, 8.3.9

author, 4.2.4

menu, 3.6.4

close tree, 10.28.5

secondary structure, 8.3.2

play slide, 7.13

translation, 8.3.3

autofit, 12.15

bioisoester, 10.9

autosave, 24.2.33

bioisostere, 10.9, 10.9.1, 10.9.2, 18.8

available properties, 10.11.1

biological, 5.4.3

ave, 19.7.1

biomolecule, 3.6.5, 5.4.3, 23.3.8, 23.3.12

avi, 6.16, 6.16.2

bit, 24.1.3

axes, 19.4.15

blast, 4.16.4, 8.4

axis, 19.4.11

search, 4.16.4

options, 19.4.10

blood brain barrier, 10.11.6

grid, 19.4.10

blue lines, 8.2

range, 19.4.10

boat, 24.5.20

title, 19.4.10

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, 9.8.8

b-factor, 5.7.5, 23.3.10

affinity model, 9.8.4

coloring scale, 24.2.38

co fold complex, 9.8.1

backbone, 6.1.10, 24.2.13

folding, 9.8

background, 6.4.2, 6.4.3

confidence model, 9.8.3

color shortcut, 24.2.2

conformations, 9.8.2

images activeicm, 7.15

diffusion stack, 9.8.2.1

image, 6.4.3

multiple sequences, 9.8.1.1

backup, 3.6.2.11

reference, 9.8.8

bad, 10.11

run gpu, 9.8.6

groups, 10.4.9

weights update, 9.8.5

ball, 4.20.5

boltz2, 9.8, 9.8.8

and stick, 3.7.1

bond, 5.1.3, 5.3.1, 5.3.1.1, 5.3.1.2, 9.11, 10.4.10, 24.4.1, 24.8.7, 24.8.10

balloon, 19.4.26

covalent, 24.4.2

bases, 10.4.6

type, 5.1.3.1, 5.1.3.2, 10.7.1, 10.7.2, 10.7.3

basicsel, 4.6.2

bonding, 6.1.8

set, 16

preferences, 4.20.1

batch, 12.3.2, 14.2.3.6

box, 4.20.7, 6.8.16, 8.7.7, 8.7.7.1, 24.5.9

file, 12.3.2.2

alignment, 23.4.4

index, 12.3.2.4

size, 18.9.1

loaded icm object, 12.3.2.1

browse, 10.3.31, 12.7.5, 21.4

mol mol2, 12.3.2.3

mode, 10.3.31

molcart, 12.3.2.5

molt, 20.2

build, 6.10.7.1

chembl, 4.16.2, 4.16.3

2D qsar, 11.1.2

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, 19.7.1, 23.6.4, 24.8.4, 24.8.5, 24.8.7, 24.8.8, 24.8.9, 24.8.10

homology model, 9.1.2

clustering, 10.28, 10.28.6

hydrogens, 9.23.5

descriptors, 24.8.15

buried molSurface, 12.7.7.4

dictionary, 10.4.4, 10.4.5, 10.4.6

buttons, 7.14

draw, 23.6.1

bye, 3.6.1.19

spreadsheet tutorial, 23.6.1

alpha, 6.1.10

edit buttons, 10.4.11

trace, 6.1.10

editor, 10.4, 10.4.8

ca-trace, 6.1.10

not starting, 24.1.13

cache, 7.14.1

fingerprint, 17

calculate, 10.11, 24.5.2

fingerprints, 24.8.15

properties, 10.11

fragments, 10.3.33

sequence similarity, 8.7.15

group, 10.4.5

startup, 24.10.2

groups, 10.4.5, 10.4.8

carbon, 24.2.4, 24.2.5

modifiers, 10.35.2

carboxylic acid, 10.15

properties, 23.6.4

cartesian, 10.23

right click, 10.4.3

cation, 5.3.2

search, 10.5, 13.2

cavities, 5.6

filter, 10.5.2

closed, 5.6.4

text, 10.5.4

ccp4, 24.2.27, 24.2.28

sketch, 23.6.1

cell, 5.4.2

space, 10.30

center, 3.6.3.20, 4.4, 6.12, 6.12.5, 18.3.13, 19.1.40, 24.4.22

spreadsheet, 4.16.2, 10.1.3, 10.3.1, 10.4.14, 23.6.1, 24.8.13

on ligand, 18.3.13

compare, 10.3.22

and representative members, 19.7.2

template, 10.3.2

cereblon, 14.3

spreadsheets, 10.3

chain.breaks, 24.2.34

substituent, 10.9

chair, 24.5.20

substructure, 4.2.2

change box size, 18.9.1

table, 18.10, 24.8.11

height of all rows, 19.1.7

display, 10.3.3

ligand, 18.5.1

tables, 19.2

residue number, 9.2

toxicity, 10.11.3

row height, 19.1.7

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, 12.7.7.4, 24.4.1

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, 24.4.1

groups, 12.2.1.3, 24.5.22

display.fit, 24.8.13

states, 9.13, 9.13.1

draw, 10.4.1

check box, 7.6.6

duplicates, 10.3.21

convert, 24.8.5

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

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

cluster, 9.23.18, 12.5.7, 12.7.7.5, 19.7.1

structure, 10.4.13

stack, 9.23.18

superposition, 10.37.3, 10.37.7

representative.center, 10.28.2

table, 10.3, 19.2

clustering, 19.7, 23.6.3

cheminformatics, 10, 10.3, 24.8

cns, 10.34

tutorials, 23.6

co-folding, 9.8, 9.8.1

chemistry, 10.24, 24.8

collada, 3.7.6, 6.3.7

convert, 10.20

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, 19.1.45, 19.7.4, 24.2.4, 24.2.5, 24.2.16, 24.2.20

2dto3d, 10.20.1

alignment, 8.7.9

pca, 10.29

background, 6.4.2

smiles, 10.20.3

by, 6.4

duplicates, 10.33

alignment, 8.8

remove.redundant, 10.33

chemical, 10.3.35

chemlib.so, 24.1.3

faq, 24.2.20

chemspace, 10.5.5

key, 24.2.38

append, 23.6.4.4

scale, 24.2.38

build visualize, 23.6.4.1

surface by proximity, 6.3.3

compare, 23.6.4.8

selection, 6.3.4

delete row, 23.6.4.3

table, 10.3.27

distinguish, 23.6.4.7

2D sketch, 10.5.6.5

export, 23.6.4.5

background, 3.6.3.18, 6.4.2

project, 23.6.4.6

distance, 6.8.10

select, 23.6.4.2

mesh, 6.3.9.3

chi, 6.8.5, 24.2.18

table, 10.3.27

chimeric ligands, 12.13

coloring, 6.4.1

chiral, 10.25, 12.1.3

column, 19, 19.1.6, 19.1.22, 19.1.25, 19.1.39, 19.1.40, 19.4, 19.4.1, 24.8.7

chirality, 10.25, 12.1.3

annotation, 19.1.41

considerations, 12.1.3

order, 19.1.29

chrome, 24.3

plot, 19.4.6

cis trans proline, 23.5.2

row width, 19.1.22

clash, 4.20.5, 6.8.15

statistics, 19.1.32

volumes, 12.7.7.8

visibility order, 19.1.28

classes, 10.3.28

color, 19.1.10

classification model, 17.5

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, 23.6.8

click, 4.13, 6.11, 6.12

combine, 3.6.10.5

clip, 6.3.10, 6.13.1, 24.2.11

display style, 4.20.9

clipboard, 6.15.3, 19.7.3

command, 24.5.16

clipping, 24.2.19

line, 9.8.7.3, 24.2.32

planes, 6

commands, 24.10.1

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, 18.23

table, 10.3.22

downstream cluster, 10.28.5

tables, 10.31

project, 18.23

compatible, 3.6.1.10

cavities, 5.7.7

complex, 9.8.1, 10.6, 12.7.7.3

cloud, 12.5.7, 12.5.7.2

compound, 4.2.4, 10.24, 19.2

compress, 4.20.6

cpk, 6.1.5, 24.2.21

compressed, 19.1.6

crash, 3.6.2.11

table view, 19.1.6

creat, 7.6.1

conditions, 10.5.2

create, 19.1.1

gen, 10.23

markush, 10.35.3

confidence, 9.8.3

new objects, 4.17

configuration error, 24.1.19

cross, 24.2.10

conformation, 9.23.18, 10.23, 12.9.2

section, 6.13

conformational entropy, 10.27

cryptic, 5.7.7

stack, 16

crystal, 5.4.2

conformations, 9.8.2, 24.9.8

crystallographic analysis, 5.4

conformer energies, 16

biomolecule, 5.4.3

conformers, 10.23

contour map, 5.4.6

connect, 6.3.9.1, 6.12, 6.12.7

convert2grid, 5.4.7

object, 6.12.7

crystallographic cell, 5.4.2

connectivity, 10.4.3, 10.5.1

load eds, 5.4.4

consensus, 10.38, 23.8.2

maps cell, 5.4.5

pharmacophore, 10.38.1

symmetry packing, 5.4.1

construct, 3.6.1.1, 6.10.7.1

tools, 23.3.8

molecule, 3.6.1.1

cell, 3.6.5

object, 3.6.1.1

neigbor, 5.4.1

contact, 5.6, 5.6.3, 23.3.5

neighbors, 3.6.5

surface, 6.3.2

crystallography, 5.4.4, 5.4.6, 5.4.7, 24.2.27, 24.2.28

contacts, 6.3.3, 6.3.4, 10.6, 12.7.7.6, 18.3.12

csv, 10.2.3, 19.1.2, 19.1.3, 19.1.21, 21.2

contour, 5.4.6, 5.4.7

current, 24.2.22

convert, 5.1.2, 10.20.1, 10.20.5, 24.8.5

slide, 7.13

chemical, 10.3.24

curves, 19.4.5

2D 3D, 10.7

custom, 6.12, 10.3.3, 10.37

3D molecular editor, 10.4.16

actions, 19.1.40

from pdb, 5.1.3

fragments, 10.13

local database, 3.6.1.6

label, 6.8.8

pdb, 5.1.2, 23.3.2

rotation, 6.12.2

chem, 10.7.1

customized MPO score, 10.34.1

smiles to 2D, 24.8.11

cut, 19.1.35

local.database, 3.6.1.6

vertical alignment block, 8.3.11

smiles, 10.20, 10.20.3, 10.20.4

cyclic peptide, 9.22

coordinates, 10.1.3

cys, 5.7.3

copy, 10.3.25, 10.4.11, 10.4.18, 10.5.6.2, 19.1.35

cysteine reactivity, 5.7.3

cell, 19.1.36

dG_bind_pred, 9.8.7.2

chemical, 10.3.25

damaged skin, 24.1.12

loop, 9.5

dash, 24.2.12

paste row, 19.1.35

database, 8.4, 10.10, 10.35.4, 12.5.3, 12.5.6, 20.1, 21

row, 19.1.36

file format, 12.5.3

rows, 19.1.44

search and alignment, 8.4

selection to table, 19.1.37

databases, 24.9.3

chemical, 10.3.16

novo, 12.14

covalent, 18.10.1

design, 12.13

bond, 5.7.3, 23.9.3

decompose.library, 23.6.9

docking, 12.11, 12.11.1, 18.16, 23.9.3

decomposition, 10.35.4, 10.36.1, 19.4.25

tutorial, 23.9.3

decoration, 18.18

delete, 3.6.2.1, 4.6.6, 7.6.8, 24.4.9

dimensional, 24.8.6

alignment, 8.7.5

directories preferences, 4.20.2

all, 3.6.2.2

directory, 4.20

column row, 19.1.38

disappearing labels, 24.1.12

label, 6.8.9

dislay ligand receptor interaction, 10.6

alignment, 8.7.5

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, 24.2.4, 24.2.5, 24.2.8, 24.2.10, 24.2.11, 24.2.17, 24.2.21, 24.2.30, 24.2.32, 24.4.10, 24.4.11, 24.4.20, 24.8.4

all, 3.6.2.2

chemical, 6.8.11

angle.label, 6.9.4

delete distances, 6.9.4

column, 19.1.38

dihedral, 6.9.3

distance.label, 6.9.4

distance restraints, 6.8.14

label, 6.8.9

distance2, 6.9.1

row, 19.1.38

angles, 6.9

selection, 3.6.2.1

formal charge, 6.1.9

tether, 9.23.5

gradient, 6.8.17

dendrogram, 10.30.1

hbond, 12.7.7.3

denoising, 9.8.2.1

hbonds, 12.7.7.4, 18.3.4

denovo, 12.13

hydrogen, 6.1.7

guide 1, 12.13.1

atoms ligand editor, 18.3.3

10, 12.13.4.2

mesh, 6.3.5

11, 12.13.4.3

meshes, 6.3.8

12, 12.13.5

options, 18.3

13, 12.13.5.1

planar angle, 6.9.2

14, 12.13.5.2

tab, 3.7.1, 24.2.16

15, 12.13.5.3

tether, 6.8.13

16, 12.13.5.4

toggle, 6.8.16

17, 12.13.6

CPK, 6.1.5

18, 12.13.7

angle, 6.9.2

2, 12.13.2

chemical, 10.3.3

3, 12.13.3

dihedral.angle, 6.9.3

4, 12.13.3.1

distance, 6.8.10, 6.8.14, 6.9.1

5, 12.13.3.2

electrostatic, 3.6.3.21

6, 12.13.3.3

energy.gradient, 6.8.17

7, 12.13.3.4

hydrogen, 6.1.7

8, 12.13.4

polar, 6.1.7

9, 12.13.4.1

macroshape, 6.3.6

density, 5.4.4, 5.4.6, 5.4.7, 24.2.27, 24.2.28

meshes, 6.3.5

functional theory, 16

and display.macroshape, 3.7.6

depth, 6.3.12, 6.10.5

molecule, 10.3.24

deselect, 24.2.7

origin, 6.8.12

design loop, 9.4, 9.23.10

potential, 3.6.3.21

deviation, 24.4.7

representations, 3.7.1

dfa, 17.3.3

restraints, 6.8.14

dfz, 17.3.2

ribbon, 6.1.3

dialog, 7.6.5, 9.8.7.1

skin, 6.1.4

diffuse, 3.7.2

status, 24.2.32

diffusion, 9.8.2.1

surface, 6.1.6, 6.3.1

docking, 9.8.7

surfaces, 3.7.6

model, 9.8

table, 10.3.3

dihedral, 5.6.8, 6.8.5, 24.2.18

tethers, 6.8.13

angle, 5.6

wire, 6.1.1

distance, 5.6, 5.6.6, 6.8.10, 6.9, 10.31, 24.2.12, 24.4.8, 24.4.10

sampling, 24.5.20

faq, 24.4.10

stack, 12.7.6

restraint, 12.8

template, 12.10

label, 4.20.7

document, 7.6.4, 7.6.5

distances, 3.7.3

navigation, 7.6.7

disulfide, 9.11, 9.18

documents, 6.15.3

bonds, 9.18

dollar, 24.10.3

diverse set, 19.7

donator, 10.4.9

dock, 12, 12.15, 18.10, 18.10.1, 23.9.3, 23.11.1, 23.11.2, 23.12.1, 24.5.3, 24.5.4, 24.5.5, 24.5.7, 24.5.8, 24.5.10, 24.5.11, 24.5.12, 24.5.13, 24.5.14, 24.5.15, 24.5.16, 24.5.21

envelope, 3.7.1

apf, 18.17

surface, 4.20.5

chemical table, 12.3.4

dotted line, 6.1.3

command, 24.5.16

lines, 24.2.34

macrocylce, 24.5.20

double, 10.4.10

start, 12.1

doublet, 10.4.7

table, 18.10

download, 24.1.1, 24.9.3

covalent, 18.10.1

dpc, 17.3.4

docked ligand strain, 12.1.10

drag, 4.12, 4.20.7, 6.8.3, 7.6.4, 8.6.6, 24.4.5

docking, 5.7.6, 12, 12.1, 12.2, 12.2.1, 12.5, 12.5.1, 12.5.2, 12.5.6, 12.6, 12.7.2, 12.9, 12.9.1, 12.9.2, 12.9.3, 12.12, 14, 14.2, 14.2.1, 14.2.2, 14.2.3, 14.2.3.1, 14.2.3.2, 14.2.3.3, 14.2.3.5, 14.2.3.6, 14.2.3.7, 18.10, 18.10.1, 18.11, 23.9, 23.9.1, 23.9.2, 23.11.3, 23.12, 23.12.2, 24.5, 24.5.1, 24.5.9, 24.5.17, 24.5.18

and drop sequences, 8.6.6

batch index, 12.3.2.4

residue label, 3.6.3.16

covalent, 12.11

draganddrop, 4.12

display, 12.7.3

draw, 10.4.18, 10.35.5, 24.8.2

explicit group, 23.12.2

chemical, 10.4.1

from table, 12.3.1.1, 12.3.1.2

drop, 4.12, 7.6.4, 8.6.6, 24.4.5

macrocycles, 12.2.1.3

drug, 10.11, 24.8.7, 24.8.9

maps, 12.2.1.1, 12.2.1.2

bank, 4.16, 4.16.7, 10.1

preferences, 12.2.1.3

like, 10.11.6

database scan, 12.2.1.3.2

drugbank, 10.1

display, 12.2.1.3.3

druglikeness, 10.4.9

general, 12.2.1.3.1

dsPocket, 4.9

project, 9.8.7.1, 12.5.5

dual alanine scanning, 12.9.4

table, 12.5.5

easy rotate, 3.6.3.12

results display, 12.7.3

ecfp, 11.3

setup, 24.5.13

edit, 5.3.1.1, 18.5.8, 24.8.3

start, 12.2.1

2D, 18.5.1

steps, 12.2

add sequence, 10.4.17

template, 12.10

alignment, 8.7.1

guide 1, 12.10.1

chemical moledit, 10.3.26

2, 12.10.1.1

ligand, 18.5, 18.5.1

3, 12.10.1.2

2D, 18.5.1

templates, 18.12.3

editor preferences, 18.2

tutorials, 23.9

multiple substituents, 18.5.2

waters, 12.1.8

tools, 3.6.2.17

background, 24.5.19

menu, 3.6.2

batch, 12.3.2

molecular document, 7.6.1

conformations, 24.5.20

molecule, 10.4

flexible.rings, 24.5.20

molt, 20.3

interactive, 12.3.1

selection, 3.6.2.5

preparation, 12.2.1

slide, 7.4.1

procedure, 12.3

table row, 19.1.24

results, 12.7, 12.7.5, 12.7.6

molecule, 10.3.26

editor, 24.4.12

errno, 24.1.3

editpdbsearch, 3.6.2.12

error, 24.1.3, 24.1.19, 24.2.35

eds, 5.4.4, 5.4.6, 5.4.7

evaluate score strain, 18.4

effect of mutation, 9.16, 9.17

exact, 10.31

on binding tutorial, 23.5.3

excel, 10.2.3

example2, 23.5.3.1

exclude fragment, 10.5.2

stability tutorial, 23.5.4

volume, 18.3.11

effort, 10.23, 10.37, 24.5.12

exit, 3.6.1.19

electron, 5.4.4, 5.4.6, 5.4.7, 24.2.27, 24.2.28

point, 18.19

denisty map, 5.4.5

explicit, 10.3.28, 12.9.1

density map, 3.6.1.7, 3.6.5, 5.4.4, 5.4.6, 12.15

flex, 12.9.1

contour, 3.6.5

group, 12.9.3

electrostatic coloring scale, 24.2.38

docking, 12.9.3

potential, 3.6.3.21, 16

groups, 23.12.2

surface, 6.3

export, 5.6.10, 21.4

electrostatics, 6.3.1, 14.2.3.5

dock project, 18.22

elegant sketch, 6.10.4

pdb, 4.19

element, 10.4.10

extra windows, 6.2

eln, 21.7

extract, 4.18.2, 8.1, 10.1.3, 24.4.12, 24.8.8

embed browser, 7.11

2D, 10.1.1

powerpoint03, 7.8

3d coordinates to spreadsheet, 10.1.3

powerpoint07, 7.9

icb, 3.6.1.5

powerpoint10, 7.10

object icb, 4.18.2

activeicm, 7.13

sub alignment, 8.3.10

script, 7.13

icb, 3.6.1.5

browser, 7.7, 7.11

pharmacophore, 10.5.6.4

firefox, 7.7, 7.11

faq, 24, 24.2, 24.2.13, 24.4, 24.5, 24.7, 24.10, 24.10.2

internet.explorer, 7.7, 7.11

ISISdraw, 24.8.3

microsoft, 7.7

MolCart, 24.9

powerpoint, 7.7, 7.8, 7.9, 7.10

activeicm, 24.3

empty hostid, 24.1.18

path, 24.3.3

enamine, 10.5.5

alignment secondary structure, 24.6.2

real, 12.6

apf model, 24.8.12

enantiomer, 24.5.21

atom charge, 24.4.21

enantiomers, 12.1.3

display, 24.2.17

endocyclic torsion angles, 5.6.12

autosave, 24.2.33

energy, 5.7.4, 6.8.15, 10.27, 10.27.2, 12.7.6, 24.5.1, 24.5.2, 24.9.8

backbone, 24.2.13

circles, 12.7.7.8

background color, 24.2.2

maps, 12.2.1.1, 12.2.1.2

job, 24.5.19

minimization, 16

beep, 24.2.35

terms, 9.23.19

binding energy, 24.5.2

ensemble, 12.9.2

blend transition, 24.2.31

calculations, 9.23.18

breaks, 24.2.34

entropy, 10.17, 10.27.1

change torsion, 24.4.16

enumerate formal charge states, 10.18

chem table display, 24.8.4

reaction, 23.6.10

chemical monitor, 24.8.10

enumeration, 10.35.4

query2, 24.8.1

eps, 10.2.6

cheminformatics, 24.8

epsilon, 24.4.15

clipping plane, 24.2.11

eraser, 10.4.11

closest, 24.4.22

skin, 24.2.16

plist, 24.1.9

command line display, 24.2.32

pmf score, 24.5.6

convert chemical from pdb, 24.4.1

pockets, 24.2.14

covalent bond, 24.4.2

preserve coordinates, 24.8.6

delete, 24.4.9

quad buffer, 24.1.7

descriptors, 24.8.15

receptor selection, 24.5.14

deselect, 24.2.7

reload dock, 24.5.4

dihedral, 24.2.18

remove salt, 24.8.14

dock charge groups, 24.5.22

select, 24.2.6

probe, 24.5.13

renumber, 24.4.4

racemic, 24.5.21

residue number selection, 24.2.36

repeat, 24.5.5

rmsd, 24.4.7

working directory, 24.5.23

rmsdtips, 24.4.8

docking, 24.5

rocking active ppt, 24.3.1

docktime, 24.5.11

speed, 24.3.2

dollar, 24.10.3

rotate chemical, 24.8.13

download install, 24.1.1

scale display, 24.2.38

druglikeness, 24.8.9

scanScoreExternal, 24.5.17

energy, 24.5.1

scanScoreExternal2, 24.5.18

error admin, 24.1.10

score, 24.5.8

extract ligand, 24.8.8

script, 24.10

flexible dock, 24.5.15

sequence secondary structure, 24.6.1

ring docking, 24.5.20

alignments, 24.6

font size, 24.2.1

smiles, 24.8.11

foreground table, 24.10.4

solvent accessible surface table, 24.4.19

gl failure, 24.1.11

ss, 24.4.17

gui, 24.2

structure, 24.4

guided dock, 24.5.3

superimpose, 24.4.6

hitlist, 24.5.7

surface display, 24.2.37

hydrogen bond acceptors, 24.8.17

thoroughness, 24.5.12

iSee, 24.2.30

transparent ribbon, 24.2.3

icmPocketFinder, 24.5.10

truncate mesh, 24.2.15

insert column, 24.8.7

view stack, 24.9.8

installation, 24.1

weak hydrogen bonds, 24.4.20

interactions, 24.2.12

write pdb, 24.4.3

ligandbox, 24.5.9

faqcontour, 24.2.28

measure distance ring, 24.8.16

faqhbondstrength, 24.2.29

merge, 24.4.5

faqmaps, 24.2.27

modeling, 24.7

faqoda, 24.2.26

molcart 64bit, 24.1.3

faqstereo, 24.1.14

query, 24.9.5

fasta, 8.1.5

sdf, 24.9.4

fbdd, 12.12

text search, 24.9.6

fft, 14.2.1

molecule c, 24.2.5

protein protein docking, 14.2.1

moledit, 24.8.2

file, 3.6.1.3

movie planes, 24.2.19

close, 3.6.1.13

newscript, 24.10.1

compatible, 3.6.1.10

nmr, 24.4.18

export, 3.6.1.12

nvidia error, 24.1.2

high quality image, 6.15.1

origin, 24.2.10

load, 3.6.1.7

password, 3.6.1.11

multiple chain, 9.1.3.1

preferences, 3.6.1.16

refinement, 9.1.3

quick image, 3.6.1.14

scene antialias, 3.6.3.10

icb, 4.11

screen, 3.6.3.8

recent, 3.6.1.17

function, 19.1.26, 19.1.32

bak, 3.6.2.11

functional, 16

filter, 20.2, 24.2.4

groups, 10.13

selection, 4.6.8

furanose ring conformation, 5.6.12

filters, 12.5.5

fuzzy, 12.10

find chemical, 10.3.32

gap, 9.4

fingerprint, 11, 11.3, 23.13, 24.8.1, 24.9.5

general preferences, 4.20.5

method, 11.3

generalselecttools, 4.6.1

fingerprints, 24.8.15

generator, 5.4.3, 10.23

firefox, 24.3

geometry optimization, 16

fit, 10.3.34, 12.15, 24.5.15

getting started, 4

fitting, 12.15, 19.4.16

giga search, 10.5.5

five-membered ring conformation, 5.6.12

sized library, 12.6

fixed torsion, 16

gigasearch, 10.5.5

flexibility, 5.7.5, 12.9.3, 23.12

ginger, 10.23

flexible, 10.37, 12.9, 12.9.1, 12.9.2, 23.12.1, 24.5.15

glasses, 6.6, 24.1.6, 24.1.14

APF superposition to template, 10.37.4

global side-chain sampling, 9.20

docking, 18.13

glutamine proline, 9.23.2

receptor, 9.8.7

google, 3.6.1.7

groups, 18.13

objects, 6.3.7

ring sampling level, 12.2.1.3

3D, 3.7.6, 6.3.7

flood, 9.23.17

gpcr_model, 23.5.1

fog, 3.6.3.5, 6, 6.10.1

graft loop, 9.5

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, 19.1.40, 19.7.4

graphical, 24.2.4

preferences, 4.20.7

display, 5.1.3.1, 5.1.3.2, 10.7.2, 10.7.3

size, 8.7, 24.1.16, 24.2.1

tutorial, 23.1

form view, 19.1.5

2D3D labels, 23.1.4

formal, 5.1.3, 24.4.21

annotation, 23.1.2

charge, 6.1.9, 10.15, 10.18

color representation, 23.1.1

format, 19.1.2, 19.1.40

labels, 23.1.3

formula, 10.4.9, 10.11

user interface, 24.2

fragment, 10.3.35, 10.36.1, 12.4, 12.12, 18.11

graphics, 5.3, 5.3.1

linking, 18.11

card, 24.1.2

screening, 12.12

controls, 6

fragments, 10.8

defects, 24.1.12

frame, 8.3.3

effects, 6.10

free energy, 9.14, 9.15

panel, 6.2

radical, 10.4.7

preferences, 4.20.3

wilson regression analysis, 10.36.2

shadow, 3.6.3.13, 6.10.2

freedomspace, 10.5.5

green arrows, 8.7.16, 24.6.2

freeze column, 19.1.30

lines, 8.2, 24.6.1

row, 19.1.31

grid, 10.3.3, 10.37, 23.12.1, 24.8.4

frequency, 10.3.35

grob, 4.20.5, 5.4.4, 5.4.6, 5.4.7, 6.3

front, 6.3.10, 6.13.1

group, 10.36.1, 18.6

full model, 9.1.3

column, 19.1.46

builder, 9.1.3

groupGen, 18.18

guanidinium, 10.15

older versions, 9.1.1.3

gui, 4.1, 4.20.4

hover, 19.4.26

jobs, 12.5.7.1

3D editor, 23.7

menus, 3.6

add columns, 10.3.4

preferences, 4.20.4

cluster center, 10.28.2

tabs, 3.7

color 2D by ph4, 10.5.6.5

guided docking, 12.8, 24.5.3

copy 2D, 10.3.16

h-bond, 5.3, 5.3.1, 5.3.1.1, 5.3.1.2, 24.2.12

paste, 10.3.6

halogen, 10.11.2

decompose, 23.6.9

hardware stereo, 3.6.3.7, 24.1

duplicate chemicals, 10.3.21

hba, 12.7.7.7

edit table, 10.3.17

hbd, 12.7.7.7

tree, 10.28.4

hbond, 5.2, 5.3, 5.3.1, 23.3.6, 24.2.29

excel, 10.3.10

strength, 24.2.29

extract 3D ph4, 10.5.6.4

header, 4.2.7, 19.4.9

filter, 10.3.12

health, 5.7.4

find replace, 10.3.13

heatmap, 19.4.7

mark row, 10.3.14

example, 19.4.7.1

markush, 23.6.8

helix, 24.2.20

structure, 23.6.7

help, 2

merge tables, 10.3.23

videos, 2

properties, 10.3.19

hetero, 10.3.28

reactions, 23.6.10

scan, 18.7

reorder, 10.28.3

hidden block format, 8.7.11

sdf, 10.3.9

width, 8.7.11

show hide, 10.3.8

hide, 19.1.39

sort column, 10.3.5

column, 19.1.28

standardize, 10.3.18

high, 3.6.1.15

table hyperlinks, 10.3.15

quality, 3.6.3.11

print, 10.3.11

highlight new data, 10.3.7.1

activeicm, 3.3

his, 24.4.15

create molecular documents, 3.3.3

histidine, 9.23.2, 24.4.15

slides, 3.3.2

tautomer, 24.4.15

getting started, 3.3.1

histogram, 12.7.7.2, 19.4, 19.4.1, 19.4.9, 19.4.11, 19.4.13, 19.4.14, 19.4.15, 19.4.16, 19.4.17, 19.4.18, 19.4.20, 19.4.22

ppt, 3.3.4

bins, 19.4.3

web, 3.3.5

options, 19.4.2

chemical clusering, 10.28.1

bin.size, 19.4.2

icm browser convert display pocket, 3.1.4

bins, 19.4.3

distances angles, 3.1.9

color, 19.4.2

get started, 3.1.1

source, 19.4.2

graphical display, 3.1.2

style, 19.4.2

effects, 3.1.5

title, 19.4.2

images, 3.1.7

historeceptomics, 4.16.9

labels annotation, 3.1.6

hitlist, 12.5.8, 12.7, 12.7.1, 12.7.7.1, 12.7.7.5, 15.4, 24.5.7

pro crystallographic tools, 3.2.6

cluster apf, 12.7.7.5

get started, 3.2.1

columns, 12.7.1.2

graphics, 3.2.2

export, 12.7.1.4

plots, 3.2.8

homology, 4.2.3, 4.16.4, 9, 9.1, 9.1.1, 9.1.1.1, 9.1.2.1, 9.1.2.2, 9.1.3.1, 9.2, 9.3, 9.9, 23.5

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

selections, 3.1.3

image, 4.15, 4.20, 4.20.5, 6.15.3, 7.6.3, 10.2, 10.2.6, 19.4.21, 24.1.20

superimpose, 3.1.8

advanced, 6.15.3

search, 4.16

distortion, 24.1.20

hrydrogen.bond, 24.2.29

preferences, 4.20.6

html, 3.6.1.12, 4.17, 7.6.1, 7.6.7, 24.3

problem, 24.1.20

html-doc font size, 24.2.1

multiple, 3.6.1.7

hybridization, 10.4.3, 10.5.1

quality, 3.6.3.11

hydrogen, 5.3.1, 5.3.1.1, 5.3.1.2, 6.1.8, 10.4.3, 10.5.1, 23.3.6, 24.2.12, 24.8.7, 24.8.10

quick, 3.6.1.14, 6.15.2

atom display, 18.3.3

images, 6.15

bond, 5.2, 6.1.8, 10.6, 12.7.7.3, 23.3.6

impose, 12.9.2

acceptors, 24.8.17

in-a-window, 24.1.7

donor, 10.38.1

inchi, 10.20.3

label edit, 5.3.1.1

increment, 19.1.27

move, 5.3.1.2

id, 19.1.27

bonds, 5.2.1, 12.1.5

independent predictions, 9.8.2

hydrogen-bond, 5.3, 5.3.1

index, 24.9.6

bond, 10.4.9, 24.4.20

induced, 24.5.15

hydrogens, 10.3.28

fit, 12.9, 12.9.1, 12.9.3, 18.13, 23.12, 23.12.1

remove, 10.3.18

insert, 7.6.4

hyperlink, 7.6.1, 7.6.2, 19.1.40

column, 19.1.26

hyrophobic, 10.38.1

image, 7.6.3, 19.1.34

iSee, 3.6.1.5, 3.6.1.12, 4.11, 6.15.3, 23.2, 24.2.30, 24.2.31, 24.3.3

table, 19.1.34

icb, 4.18.2, 4.19, 24.2.30, 24.3.3

row, 19.1.33

icm, 24.3.3

script, 7.6.4

chemist howto chemical search, 3.4.3

install, 1, 10.10.1, 21.1, 24.1.3, 24.1.4

cluster, 3.4.5

installation, 24.1

combi library, 3.4.7

interaction, 5.3, 5.3.1, 5.6.3, 10.6, 24.2.12

ph4, 3.4.4

fingerprint, 12.7.7.6

plots, 3.4.8

fingerprints, 12.7.7.6

sketch, 3.4.1

lists, 12.7.7.7

spreadsheets, 3.4.2

restraint, 12.8

stereoisomers tautomers, 3.4.6

restraints, 12.8

pro 3D ligand editor, 3.5.1

interaction-strength, 5.3.1

chem3D, 3.5.2

interactions, 18.3.12, 24.5.2

chemsuper, 3.5.4

interactive, 12.3.1, 23.2

energy, 3.5.3

loaded ligand, 12.3.1.2

qsar, 3.5.5

loop, 9.1.4.2

tutorials, 3.5

modeling, 9.1.4

tutorials, 3.4

table ligand, 12.3.1.1

hanging, 24.1.13

modeling, 9.1.4

object, 5.1, 23.3.2

interface prediction, 23.10

script, 19.1.40

internal hydrogen bonds, 12.1.5

icm-crash, 24.1.13

internet explorer, 24.3

icmFastAlignment, 8.4

interrupt, 6.10.7.3

icmPocketFinder, 5.7.7, 24.2.14, 24.5.10

animation, 6.10.7.3

icmdb, 21

introduction, 1

icmjs, 7.16

invert selection, 19.1.23

icmpocketfinder, 23.3.7

invisible residue label, 24.1.12

id, 19.1.27

ionization, 9.13, 9.13.1

identity, 4.2.3

iqr, 19.4.23

isis, 10.4.18

layers, 6.14

isostere, 13.2

learn, 10.21, 10.22, 11, 11.1, 19.6, 24.8.12

isotope, 10.4.3, 10.5.1

learning, 11

iupac, 10.2.7, 10.3.20

theory, 11.5

javascript, 7.16

least.squares, 19.4.16

job, 24.5.19

library, 10.35.4

join, 10.32

reaction, 23.6.10

jpg, 6.15

license, 24.1.4

means, 19.7.1

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, 12.9, 14.2.3.3, 14.2.3.4, 18.3.12, 18.3.13, 18.5.8, 18.10, 18.11, 24.4.5, 24.4.11, 24.5.2, 24.5.9, 24.8.8

kcc, 17.3.1, 17.5

aide, 12.14

keep carboxyls neutral, 12.2.1.3

guide 1, 12.14.1

kernel regression, 17.3.1

2, 12.14.1.1

chemical, 10.4.10

3, 12.14.1.2

keyboard mouse, 6.11

4, 12.14.1.3

keystokes in chem-edit, 10.4.10

5, 12.14.1.4

kmz, 3.7.6, 6.3.7

based screen, 10.38.3, 13.1

knime, 22

screening, 13

label, 4.20.7, 5.3.1, 19.7.4, 24.2.17

best replace, 18.6

atoms, 6.8.2

binding, 9.17

color, 6.8.7

code, 4.2.4, 4.16.6

move, 6.8.4

considerations, 12.1.2

residues, 6.8.3

editor, 18, 18.10, 18.10.1, 18.16, 18.17

sites, 6.8.6

bioisostere, 18.8

variables, 6.8.5

covalent docking, 18.16

2D, 3.7.3

mrc, 18.15

3D, 3.7.3, 6.8.1

preferences, 3.6.2.18

atom, 6.8.1

energetics, 10.27

atoms, 6.8.2

conformational entropy, 10.27.1

color, 6.8.7

strain, 10.27.2

custom, 6.8.8

environment, 9.20

delete, 6.8.1, 6.8.9

optimization, 9.20

distance, 6.8.10

pocket, 5.2.1, 24.4.11

drag, 3.6.3.16

surface, 18.3.2

move, 3.6.3.16, 6.8.4

receptor contacts, 18.3.12

residue, 6.8.1

display, 5.2

residues, 6.8.3

interaction, 10.6

site, 6.8.1

strain, 18.3.10

sites, 6.8.6

surface, 5.2.3

variable, 6.8.1

tether, 18.12

variables, 6.8.5, 24.2.18

vicinity, 9.20

labeling, 6.8.1

ligand-based, 12.4, 13, 13.1

labels, 6.8, 10.3.28

ligand-induced RNA conformational changes, 5.6.12

distances, 6.8.10

convert, 9.23.1

tab, 3.7.3

editor, 18, 18.1

landscape, 4.20.6

binding.re-dock ligand, 18.9

large chemical space, 23.6.4

display, 18.3

font, 24.1.16

edit, 18.5

size, 24.1.9

energy, 18.3

sdf, 10.1.2

hydrogen.bond, 18.3

layer, 6.14

pocket, 18.3

restraint, 18.12

log, 19.4.6, 19.4.11

surface, 18.3

logD, 10.11.8

tether, 18.12

logP, 10.4.9, 10.11

optimization, 23.11.3

logS, 10.4.9, 10.11

pocket, 4.9

logarithmic, 19.4.11

receptor.contact, 5.6.3

logout, 3.6.1.19

ligand_pocket_interactions, 5.2.1

loop, 9.3, 9.5, 24.2.20

ligedit distance restraint, 18.12.2

analysis, 9.7

tab, 3.7.5

design, 9.4

tether, 18.12.1

find pdb segments, 9.7

light, 3.7.2

model, 9.3, 9.4, 23.5.2

tab, 3.7.2

tutorial, 23.5.2

lighting, 6.3.9.4, 6.5

modeling, 9.1.4.2, 9.6, 9.7, 9.23.10

likeness, 10.11, 24.8.9

preferred residues, 9.6

line, 4.20.5, 19.7.4, 24.2.12

model, 9.23.9

lineWidth, 4.20.3

sample, 9.23.9

link, 8.3.9

energy water, 9.23.17

structure to alignment, 23.4

mac, 10.10.1, 24.1.9, 24.1.16

linker, 14.3

font, 24.1.16

links, 4.6.20

size, 24.1.16

linux, 10.10.1

machine learning, 23.13

lipinski rule, 10.34

macrocycles, 9.22

list, 4.6.18

macros, 7.14

liver, 10.11.5

macroshape, 3.6.3.22, 6.3, 6.3.6

lmhostid, 24.1.18

make, 6.10.7.1, 19.1.1

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

alignment, 8.6.1

example alignment, 8.3.14

animation, 6.10.7.1

nmr model, 4.2.5

apf docking sar model, 17.6

pdb hyperlinks, 4.2.6

complex, 12.7.7.4, 18.23

protein structure, 5.1.1

flat, 24.8.13

sequence, 8.1

molecular document, 7.6

extract pdb, 8.1.3

molt, 20.1

from file, 8.1.4

receptor maps, 12.2.1.2

paste, 8.1.2

selection, 4.6

swissprot, 8.1.1

level, 4.6.3

libraries, 9.23.6

bond, 24.4.2

local, 24.2.24, 24.2.25

disulfide, 9.11, 24.4.17

boltz diffusion, 9.8.7, 9.8.7.1, 9.8.7.2, 9.8.7.3

molecule, 3.6.1.1

command, 9.8.7.3

object, 3.6.1.1

gui, 9.8.7.1

making molecular slides, 7.1

results, 9.8.7.2

html, 7.6

databases, 20

manual change torsion, 18.5.4

minimization, 9.20

map, 4.20.7, 5.4.4, 5.4.6, 5.4.7

database.browse, 20.2

cel, 5.4.5

edit, 20.3

maps, 12.2.1.1, 12.2.1.2, 14.2.3.5, 23.12.1, 24.2.27, 24.2.28, 24.5.9

query, 20.4

mark, 19.1.45

row, 20.3

row, 19.1.45

localpdb, 24.2.24

color, 19.4.14

localseq, 24.2.25

shape, 19.4.13

lock, 6.3.10, 6.13.1, 10.3.31

size, 19.4.13

docking, 23.11.3

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, 9.9, 9.19, 23.5

library, 23.6.8

domain interaction, 9.19

mass, 24.4.22

download, 9.8.5

matched pair, 10.36.6, 23.6.11

start, 9.1.1.2

analysis, 10.36.6

weight, 11.1.4

materials, 3.7.6

modelers view, 9.1.4.1

max, 19.7.1

view, 9.1.4.1

maxColorPotential, 4.20.10

modeling, 9.23.3

maximum common substructure, 10.28.6, 10.30, 10.30.1

options, 9.1.1.1

dendrogram, 10.30.1

modeller view, 9.1.4

mcs, 10.28.6, 10.30.1

modification history, 18.5.6

rgroup decomposition, 10.28.7

modify, 9.13.2

mean, 19.4.6, 19.4.23, 24.4.7

amino acid, 9.13

measure distance, 24.8.16

group, 9.12

to ring, 24.8.16

mol, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.4.13, 23.11.2

median, 19.4.6, 19.4.23

mol2, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6

membrane, 12.1.7, 15.3

molcart, 10.10, 10.10.1, 10.10.2, 10.10.3, 10.10.4, 10.10.5, 20, 21, 24.1.3, 24.8, 24.8.1, 24.9.3, 24.9.4, 24.9.5, 24.9.6

exposed docking, 12.1.7

add database, 10.10.3

memory, 10.1.2

administration, 10.10.5

menu, 7.6.5

connect, 24.9.2

chemistry, 3.6.14

download dbs, 24.9.3

docking, 3.6.15

hostid, 24.9.1

homology, 3.6.13

installation, 10.10.1

molmechanics, 3.6.16

license, 24.1.4

tools chemical search, 3.6.11

search, 10.10.4

molecular editor, 3.6.12

start, 10.10.2

windows, 3.6.17

connect, 24.9.2

merge, 10.32, 24.4.5

hostid, 24.9.1

two sets, 10.32

license, 24.9.1

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

molclart, 24.1.4

clip, 6.3.10

molecular, 5.3, 5.3.1, 10.3.30, 10.3.31, 10.3.34, 10.3.35, 10.23, 24.8.7, 24.8.10

color lighting, 6.3.9.4

animations slides, 7

options, 6.3.9

documents, 23.2

representation, 6.3.9.3

dynamics, 15, 15.1, 15.2, 15.3, 15.4

save, 6.3.11

membrane, 15.3

options, 6.3.9

restraints, 15.2

meshes, 6.3.2, 6.10.5

run, 15.1

surfaces grobs, 6.3

vls, 15.4

tab, 3.7.6

editor, 24.8.2

metabolic oxidation, 17.7

graphics, 6

min, 19.7.1

interaction display, 5.3

minimization, 9.19

matched pairs, 23.6.11

cartesian, 9.23.8

mechanics, 9.23

global, 9.23.8

convert, 9.23.1

local, 9.23.8

design loop, 9.23.10

minimum specifications, 1

edit structure, 9.23.5

mmff, 9.23.6, 10.4.16, 24.2.17, 24.8.5

gamess, 9.23.16

type, 6.8.2

generate normal mode stack, 9.23.14

mmp, 23.6.11

his asn, 9.23.2

mnSolutions, 4.20.10

ic table, 9.23.13

minimize, 9.23.8

binary classification, 10.34.2

mmff, 9.23.6

custom step function, 10.34.1.2

regularization, 9.23.3

customized, 10.34.1

sample loop, 9.23.9

save, 10.34.1.3

peptide, 9.23.12

special cases, 10.34.1.1

protein, 9.23.11

mtl, 6.7

terms, 9.23.19

multi apf super, 10.37.7

view stack, 9.23.15

panel, 6.2

modeling, 9, 9.20, 16

parameter optimization, 10.34

table, 10.20.2

template, 9.1.4.3

weight, 10.4.9

windows, 6.2

molecule, 24.2.8, 24.8.3

multi-chain, 9.8.1.1

editor, 10.4

multiple, 12.9.2, 23.12.1

moledit, 10.4.8

chain, 9.1.2.2, 9.1.3.1

molmechanics, 24.9.8

position group scan, 18.7

minimize, 9.23.8

rec, 12.9.2

mmff, 9.23.6

receptor, 4.16.1, 23.12

molscreen, 12.4, 17

docking, 18.15

custom model panel, 17.4

sequences, 9.8.1.1

load models, 17.1.1

protein, 24.2.5

run, 17.1

mutant, 9.12, 24.4.13, 24.4.14

model type, 17.3

mutate, 9.14, 9.15, 24.4.15

results, 17.2

residue, 24.4.13

molskin, 6.3.2

N C, 24.4.14

molsynth, 10.11.7

mutation, 9.12, 9.14, 9.15, 9.17, 23.5.3, 23.5.4, 24.4.13, 24.4.14

molt, 20, 20.4

protein binding, 9.14

monitor, 24.8.10

ligand, 9.17

monochrome, 10.3.28

peptide, 9.16

montecarlo, 24.9.7

stability, 9.15

mouse, 4.4, 6.11, 6.12

mysql, 21

mov, 6.16, 6.16.2

navigate workspace, 4.6.10

move, 3.6.3.19, 4.12, 4.14, 5.3.1.2, 6.3.9.1, 6.3.9.2, 6.12, 6.12.7, 9.19, 24.4.5

nearest, 24.4.22

column, 19.1.28

neighbors, 5.3.1

mesh, 6.3.9.2

nephrotox, 10.11.4

slide, 7.4.2

neural network, 18.18

structure, 6.12

Torsion Profile Neural Network Prediction Engine, 6.12.6.1

tools, 6

new, 8.1

rotate, 6.11

icm session, 3.6.1.2

slab, 6.11

table, 19.1.1

translate, 6.11

table, 19.1.1

z-rotation, 6.11

nmr, 24.4.18

zoom, 6.11

model, 4.2.5

movie, 6.16.1, 24.2.19, 24.9.7

nnc, 17.3.5

montecarlo, 24.9.7

nntorsion, 6.12.6.1

making, 6.16, 6.16.2

nof, 10.11.2

open, 6.16, 6.16.2

chemical, 10.11.2

mpa, 23.6.11

non-contiguous selection, 4.6.18

mpeg, 6.16, 6.16.1, 6.16.2

non-covalent, 5.3

mpg, 6.16, 6.16.2

normal modes, 9.23.14

mpo, 10.34

nucleic acid conformation analysis, 5.6.12

nucleotide analysis, 5.6.12

iw, 10.7.2

conformation, 5.6.12

dormat, 4.19

geometry, 5.6.12

file, 24.4.3

puckering, 5.6.12

html, 4.2.7

number of sp3, 10.11.2

preparation, 23.3.11

numbers, 10.3.28

search, 4.2.3, 4.2.4, 23.3.1

nvidia, 24.1.2

hyperlinks, 4.2.6

obj, 6.7

convert, 9.23.1

object, 4.12, 4.19, 23.3, 24.2.8

recent, 3.6.1.18

objects, 5.1.2

search, 3.7.4, 4.2, 4.2.1

in table, 19.3

pdbsearchfield, 3.6.2.13

in.table, 19.3

pdbsearchhomology, 3.6.2.15

occlusion, 6.3.12, 6.10.5

pdbsearchidentity, 3.6.2.14

shading, 6.3.12

pdbsearcsequence, 3.6.2.16

effect, 6.10.5

peptide, 4.17, 9.16, 9.22, 14, 14.1

occupancy, 6.1.3, 23.3.10

docking, 14.1

oda, 5.7.6, 14.2, 14.2.2, 14.2.3

guide 1, 14.1.1

older version, 3.6.1.10

10, 14.1.4

omega, 6.8.5, 24.2.18

11, 14.1.5

online databases, 10.5.5

12, 14.1.5.1

open, 3.6.1.3, 4.18, 19.1.2

13, 14.1.5.2

file, 4.18

14, 14.1.5.3

password, 4.18.1

2, 14.1.2

with password, 3.6.1.4

3, 14.1.2.1

movie, 6.16, 6.16.2

4, 14.1.3

password, 3.6.1.4, 4.18.1

5, 14.1.3.1

optimal, 5.7.6, 14.2, 14.2.2, 14.2.3

6, 14.1.3.2

optimize, 9.23.2

7, 14.1.3.3

oracle, 21

8, 14.1.3.4

orange, 4.6.5

9, 14.1.3.5

selection, 4.6.5

modeling, 9.22

origin, 6.8.12, 24.2.10

editor, 18.21

orthosteric, 5.7.7

percentage similarity, 8.7.15, 23.4.4

other selection, 4.6.19

perspective, 3.6.3.9, 6.10.6

outside, 24.5.9

ph4, 10.5.6

overlay, 23.3.3, 24.2.5, 24.4.6

draw 2d, 10.5.6.1

pH, 5.7.2, 10.19

3d, 10.5.6.2

pKa, 5.7.2, 9.13, 9.13.1

search, 10.5.6.3

pLDDT, 9.8.3

pharmacophore, 10.3.35, 10.5.6.5, 13, 23.8.2

package.activeicm, 7.13

2D, 23.6.6

packing, 5.4.1

3D, 23.6.5

pages, 21.7

clone, 10.5.6.2

pairwise, 10.37.5, 10.37.6

draw2D, 10.5.6.1

apf score, 10.38

draw3D, 10.5.6.2

parallelization, 12.5.7

edit, 10.5.6.1, 10.5.6.2

password, 10.10.5

move, 10.5.6.2

paste, 10.4.11, 10.4.18, 19.1.35

new, 10.5.6.2

pca, 19.5

search, 10.5.6, 10.5.6.3, 23.6.5, 23.6.6

pdb, 3.6.1.7, 4.2.2, 4.16, 4.16.6, 4.19, 5.1.3, 10.7.1, 23.3, 24.2.24, 24.2.25, 24.4.4

phase angle P, 5.6.12

chem gl, 10.7.3

phi, 6.8.5, 24.2.18

phylogeny, 8.7.8

point label, 19.4.19

pi, 5.3.2

portait, 4.20.6

cation, 5.3.2

post edit ligand, 18.5.8

pi, 5.3.2

screen, 12.7.7

pi-pi, 5.3

postscript, 4.20.6

picking, 6

potential mean force, 12.5.4

picture, 3.6.1.14, 4.15, 6.15.2, 7.6.3

ppbatch, 14.2.3.6

tips, 4.15

ppepitope, 14.2.3.4

chart, 19.4.8

ppmaps, 14.2.3.5

pipi, 5.3.2

pprefine, 14.2.3.8

pka, 10.15

ppresults, 14.2.3.7

planar, 5.6.7, 6.8.5, 24.2.18

pproc, 14.2.3

angle, 5.6

ppsetligand, 14.2.3.3

angle, 6.9.2

ppsetproject, 14.2.3.1

plane, 6.3.10, 6.13, 6.13.1, 6.14, 24.2.11, 24.2.19, 24.2.21

ppsetreceptor, 14.2.3.2

faq, 24.2.21

ppt, 7.12, 7.14, 24.3.3

plot, 4.20, 4.20.8, 12.7.7.2, 19.4, 19.4.1, 19.4.4, 19.4.9, 19.4.11, 19.4.13, 19.4.14, 19.4.15, 19.4.16, 19.4.17, 19.4.18, 19.4.20, 19.4.21, 19.4.22, 19.4.23

predict, 8.3.2, 10.21, 10.22, 11, 11.2, 19.6, 24.8.9, 24.8.12

R group sar, 10.36.4

disulfide, 9.18

axis, 19.4.11

metabolic oxidation, 17.7

color, 19.4.14

predicting bioassays, 11.2

columns, 19.4.6

compound properties, 11.2

function, 3.6.9, 3.6.9.1

prediction binding, 9.14

grid, 19.4.15

preferences, 4.20, 12.5.5, 24.2.24, 24.2.25

header, 19.4.9

preferred residues, 9.6

inline, 19.4.22

presentation, 7.6.5, 7.7, 7.12

logarithmic, 19.4.12

presentations, 7

mark, 19.4.13

preserve, 24.8.6

mean median iqr, 19.4.23

press-and-hold to rotate, 10.4.8

point label, 19.4.19

pretty view, 18.3.6

preferences, 4.20.8

primary aliphatic amines, 10.15

groups, 19.4.25

principal component analysis, 19.5

regression, 19.4.16

regression, 11

selection, 19.4.18

components, 11.5

zoom translate, 19.4.17

print, 6.7, 19.4.20, 19.7.3

axis, 19.4.15

alignment, 8.7.4

display, 19.4.15

plot, 19.4.20

grid, 19.4.15

alignment, 8.7.4

inline, 19.4.22

printer.resolution, 4.20.6

logarithmic, 19.4.12

pro-drug, 10.26

pls, 10.21, 10.22, 11, 19.6, 23.13

probe, 12.2.1.1, 24.5.13

pmf, 24.5.6

problem, 24.1.14

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

with selection, 24.1.12

pocket, 4.9, 5.2, 5.2.2, 5.2.3, 5.7.7, 23.3.7, 24.2.14, 24.4.11, 24.5.10

prodrug, 10.26

conservation, 24.4.12

profile, 4.16.9, 8.3.8

properties, 5.9

project, 3.6.1.5, 14.2.3.1, 21.6, 23.6.4.6

surface, 5.2.2, 12.7.7.8

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, 24.8.7

pocketome, 4.16, 4.16.1, 5.9

property, 10.4.9, 24.8.7, 24.8.8, 24.8.9, 24.8.10

pockets, 5.7.7

expression, 12.7.7.4

protac, 14.3

state, 12.1.4

guide 1, 14.3.1

states, 5.7.2, 9.13, 9.13.1

2, 14.3.1.1

protonation_ph, 10.19

3, 14.3.1.2

protonation_ph_charge, 10.19.2

protect, 7.6.8

protonation_ph_concentration, 10.19.1

protein, 5.5.6, 8, 9.8, 9.16, 24.4.5

protprot, 14.2

chain, 9.4

proximity, 6.3.3, 6.3.4

complex, 9.8.1.1

psa, 10.4.9, 10.11.9

health, 5.7.4

pseudorotation P, 5.6.12

model, 9.21

analysis, 5.6.12

preparation, 9.13, 9.13.1

phase angle, 5.6.12

protein docking, 23.10

psi, 6.8.5, 24.2.18

tutorial, 23.10

pubchem, 10.1

sculpting, 9.19

publication quality images, 6.3.2

sequence, 10.4.17

puckering amplitude, 5.6.12

structure, 5

purple box, 3.6.3.23, 12.2.1.1, 18.9.1

analysis, 5.6

pyramid, 12.1.6

closed cavities, 5.6.4

pyramidal, 12.1.6

contact areas, 5.6.3

qm color by qm electrostatic potential, 16.6

distance, 5.6.6

introduction, 16.1

find related chains, 5.6.1

minimimize, 16.2

finding dihedral angle, 5.6.8

confromers, 16.3

planar angle, 5.6.7

set charges, 16.5

rama export, 5.6.10

torsion scan, 16.4

ramachandran plot, 5.6.9

hydrogen bond, 5.3.1

rmsd, 5.6.2

pdb chem gl, 5.1.3.2

surface area, 5.6.5

iw, 5.1.3.1

similarity, 5.8

qsar, 10.21, 10.22, 11.1, 23.13

tutorials, 23.3

learn predict, 10.21

analysis, 23.3.4

predict, 10.22

contact area, 23.3.5

quad buffer stereo, 24.1

convert, 23.3.2

buffer, 24.1.7

hydrogen bond, 23.3.6

quality, 3.6.1.15, 4.20.5

icmpocketfinder, 23.3.7

quantum chemistry, 16

search, 23.3.1

mechanics, 16

superimpose, 23.3.3

query, 9.1.2, 21, 21.3, 24.8.1, 24.9.5, 24.9.6

superposition, 5.5

molt, 20.4

select, 5.5.1

processing, 10.5.3

sites by apf, 5.5.6

setup, 10.5.1

superimpose 3D, 5.5.3

quick, 4.15

grid, 5.5.5

image, 6.15.2

multiple proteins, 5.5.4

model multiple chain, 9.1.2.2

protein-ligand complex, 9.20

single chain, 9.1.2.1

protein-protein, 5.7.6, 14, 14.2, 14.2.1, 14.2.2, 14.2.3, 14.2.3.1, 14.2.3.2, 14.2.3.3, 14.2.3.5, 14.2.3.6, 14.2.3.7, 23.10

start move structure, 4.4

docking refinement, 14.2.3.8

read pdb, 4.2

protein-proteindocking, 14.2.3.4

representation, 4.7

convert, 9.23.1

what is selected, 4.6.4

protonated, 24.4.15

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

table, 10.35.2

relationship, 11, 19.6

groups, 10.35.2

covalent geometry, 12.2.1.3

r-group, 10.28.7, 10.35.2

relaxed ligand, 18.3.9

decomposition, 10.28.7

reload, 12.7.2, 24.5.4

enumeration, 10.28.7

dock results, 12.7.2

r-groups, 19.4.25

remove, 24.2.6, 24.2.7, 24.2.10

racemic, 10.3.28, 10.20.5, 24.5.21

salt, 24.8.14

radar, 19.4.6

explixit.hydrogens, 10.12

rainbow, 4.20.5, 6.8.16, 10.3.35, 24.2.38

salt, 10.12

ramachandran plot, 5.6, 5.6.10

rename, 19.1.25

random forest, 11, 23.13

column, 19.1.25

range, 6.10.7.2

project, 3.6.1.9

rapid isostere replacement, 13.2

renumber, 9.2, 24.4.4

ratio.selection, 4.20.5

reorder column, 19.1.29

dock ligand, 18.9

replace chemical, 10.3.32

reactions, 10.8, 10.35.5

replacement, 18.6

reactive cysteine, 5.7.3

group, 18.8

reactivity, 10.11.3

report, 21.3

read, 3.6.1.3, 3.6.1.17, 4.18, 8.1, 10.3.1

representation, 3.6.3.19

chemical, 10.1

residue, 4.20.7, 24.2.8, 24.4.15, 24.4.22

spreadsheet, 10.3.1

alternative orientation, 23.3.11

split, 11.1.1

content, 8.3.1

table, 19.1.2

names, 9.13, 9.13.1

pdb, 4.2, 4.2.1

number selection, 24.2.36

table, 19

pKa prediction, 5.7.2

reagent, 10.35.5

pka, 5.7.2

rear, 6.3.10, 6.13.1

range, 4.6.18

recent files, 3.6.1.17

content, 3.6.4, 8.3, 8.3.1

pdb codes, 3.6.1.18

mutate, 24.4.13, 24.4.14

receptor, 5.2.2, 5.2.3, 5.3, 5.3.1, 10.6, 12.1, 12.9.2, 14.2.3.2, 14.2.3.4, 18.3.12, 23.12.1, 24.5.2, 24.5.14, 24.5.15

residues, 5.2.2, 5.2.3, 24.2.14

considerations, 12.1.1

resize, 6.3.9.1, 6.15.3

flexibility, 18.15

mesh, 6.3.9.1

pocket, 18.3.1

resolution, 4.2.4

surface, 18.3.1, 18.3.2

restore, 3.6.2.11, 6.3.10, 6.13.1

refinement, 9.20

default, 24.1.9

flexibility, 23.12.2

recent backup, 3.6.2.11

recover, 3.6.2.11

restrained docking, 12.8

cylinders, 8.7.16, 24.6.2

restraint, 18.12.1, 18.12.2

lines, 8.2, 24.6.1

restraints, 15.2

redo, 3.6.2.10, 10.4.11, 18.5.5

results, 14.2.3.7

reference, 9.8.8

stack, 12.7.6

refine, 9.9, 9.10

retrieve columns, 24.5.24

loops, 9.1.3

from original database, 24.5.24

side chain, 9.10

review and adjust binding site, 12.2.1.1

sidechains, 9.1.3

rgroup, 10.35.4

refinement, 12.9.4

ribbon, 3.7.1, 4.20.9, 6.1.3, 24.2.23, 24.2.34

region, 14.2.3.4

as a mesh object, 24.2.3

regression, 10.36.2, 11.1, 11.5, 19.4.16, 23.13

faq, 24.2.23

regul, 9.9

preferences, 4.20.9

regularization, 9.9, 9.23.3

style, 4.20.9

cylinders, 6.1.3

sample, 9.21, 10.37

smooth, 6.1.3

double bond cis trans, 12.2.1.3

worm, 6.1.3

ligand pocket, 9.20

ribbonColorStyle, 4.20.9

peptide, 9.22, 9.23.12

ribose pseudorotation, 5.6.12

protein, 9.21, 9.23.11

pucker, 5.6.12

racemic centers, 12.2.1.3

ring, 5.6.12

sar, 10.28.7, 10.36, 19.4.25

conformation, 5.6.12

analysis, 10.36

torsion angles, 5.6.12

table, 10.36.3

ride, 13.2

save, 4.19, 6.3.11, 6.10.7.4, 8.1.5, 10.2.3, 19.4.21, 19.7.3, 24.2.33

gpu benchmark, 13.2.3

SMILES, 10.4.15

server setup, 13.2.2

alignment, 8.7.3

setup, 13.2.1

PDB, 4.19

ridge, 12.6

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, 18.20

ring, 5.3.2, 10.4.3, 10.4.6, 10.5.1

file, 4.19

stacking, 5.3.2

hits, 18.5.7

rings, 10.3.28, 10.23, 10.37

image plot, 19.4.21

rmsd, 5.6, 5.6.2, 24.4.7, 24.4.8

ligand receptor complex, 18.20

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, 24.4.7

project icb, 4.11

mean square deviation, 5.6.2

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, 24.8.13

slide, 7.4

chemical, 10.3.34

smiles string, 10.4.15

torsion, 6.12.6.1

table, 19.1.21

when pasting, 10.4.8

spreadsheet, 18.5.7

easy, 3.6.3.12

tree, 19.7.3

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, 5.6.11

password, 3.6.1.11

rough surface, 24.2.37

picture, 3.6.1.15

row, 19, 19.1.22, 19.1.35, 19.1.45

project, 3.6.1.8, 3.6.1.9, 3.6.1.10, 4.11

flag, 19.1.13

table.view, 19.1.8

height, 19.1.7, 24.2.39

saving, 3.6.1.8

mark, 19.1.13

project, 3.6.1.8

hide, 10.3.8

scaffold, 10.14

show, 10.3.8

hopping, 18.8

ruler, 6.8.16

scale, 4.20.5, 24.2.38

molscreen, 17.1.2

scan, 9.23.7, 12.7.5

rundock, 24.5.16

hits, 12.7.5

rxn, 10.4.13

group, 18.7

safari, 24.3

scan_pockets, 5.9

sali, 10.36.5

scarab, 21

bridge, 23.3.6

add user, 21.5

salts, 10.3.18

browse export data, 21.4

new project, 21.6

object, 4.6.3

pages, 21.7

purple.box, 3.6.3.23

query, 21.3

residue, 4.6.3

upload data, 21.2

workspace, 4.6.3

scare, 12.9.4

selectall, 3.6.2.3

scatter, 12.7.7.2

selecting.neighbors, 4.6.16

score, 12.5.8, 12.7.1.2, 18.4, 23.8.3, 23.8.5, 24.5.7, 24.5.8, 24.5.18

selection, 4.6.4, 4.6.5, 4.6.21, 6.3.4, 10.4.11, 19.4.18, 19.7.2, 19.7.4, 24.2.4, 24.2.6, 24.2.7, 24.2.8, 24.2.13, 24.2.32, 24.4.9, 24.4.10, 24.4.22, 24.5.14

threshold, 12.5.4

clear, 3.6.2.7

screen, 10.38, 23.8.4, 23.9, 23.11.1

neighbors, 3.6.2.8

screening, 12.5, 12.5.1, 12.5.2, 12.6, 15.4, 23.12

alignment, 4.6.19

screenshot, 6.16, 6.16.2

all, 3.6.2.3

movie, 6.16.2

alter, 4.6.7

script, 4.17, 7.6.4, 7.6.5, 24.4.19, 24.10, 24.10.1, 24.10.2, 24.10.3

atom, 3.6.2.5

sculpting, 9.19

basic, 4.6.2

sdf, 10.2, 10.2.2, 10.2.4, 10.2.5, 10.2.6, 10.3.35, 10.10, 10.10.3, 10.20.1, 18.10, 20.1, 21.2, 23.11.2, 24.9.3, 24.9.4

change, 4.6.7

to hitlist, 12.7.4

clear, 3.6.2.7

search, 5.8, 10.10, 10.10.4, 20.2, 21.3, 24.9.6

column, 19.1.23

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, 19.1.23

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, 19.1.23

sequence, 4.2.3

residue, 3.6.2.5

tautomer, 10.5.3

row, 19.1.23

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, 5.5.1

structure, 5.7.1, 24.2.20

table, 4.6.19, 19.1.23

structure, 3.6.4, 6.1.3, 8.3, 8.3.2

elements, 19.1.23

select, 4.6.12, 4.6.13, 19, 19.1.45, 24.4.22

tools, 4.6.1, 4.6.2, 4.6.7, 4.6.8

a tree branch, 19.7.2

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, 9.8.1, 10.4.17, 23.3, 23.4, 23.4.4, 24.4.12, 24.6, 24.6.1

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, 19.7.2

pattern, 4.2.3

atom, 4.6.3

reordering, 8.7.8

graphical, 4.6.3

secondary structure, 8.2, 24.6.1

sites, 8.5

sampling, 14.2.3.8

structure, 8.3.6

side-chains, 12.9.1

type, 8.3.4

sigmaLevel, 5.4.6, 5.4.7

DNA, 8.3.4

similarity, 10.31, 13

alignment, 8.3.5, 8.6.2, 8.6.6

simulation, 15, 15.1, 15.2, 15.3, 15.4, 24.9.8

amino acid, 8.3.4

length, 24.5.12

nucleotide, 8.3.4

simulations, 24.7

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, 16

sequences, 8, 24.2.25

singlet, 10.4.7

unique, 8.3.13

sites, 5.5.6

extract, 8.3.13

size, 5.3.1.1

unique, 8.3.13

sketch accents, 6.10.3

server, 12.5.7.2

markush, 10.35.1

error, 24.1.17

reaction, 12.11.1

set, 10.3.31, 24.4.21

smiles, 10.4.12

formal charges, 10.15

accents, 3.6.3.14, 6.10.3

server, 24.1.17

skin, 3.7.1, 6.1.4, 24.2.16

bond type, 9.23.5

slab, 6.3.10, 6.13.1

charges, 9.23.6

slice, 6.13

chirality, 9.23.5

slide, 6.10.7.4, 7.2, 7.3.1, 7.6.1, 24.2.31

disulfide, 9.11, 24.4.17

effects, 7.5

bond, 9.23.5

movie, 6.16.1

formal charge, 9.23.5

file, 7.2

tether, 9.23.5

navigation, 7.3.2

types, 9.23.6

show, 7.3

setAPFparams, 24.8.12

blend, 7.5

setup, 14.2.3.3

edit, 7.4.1

ligand receptor, 18.1

effect, 7.5

shade, 8.7.7, 8.7.7.1

smooth, 7.5

alignment, 23.4.4

transition, 7.5

shading, 6.3.12

slides, 6.16.1, 7, 7.1, 7.3, 24.2.30

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, 24.2.20

surface, 24.2.37

shell preferences, 4.20.10

solid, 6.3.9.3

shift, 6.8.3

solvent.accessible.area, 24.4.19

shine, 3.7.2, 4.20.5

sort hitlist, 12.7.7.1

shineStyle, 4.20.3

table, 3.6.10.4

show, 7.3.1, 19.1.39

sorting, 12.7.7.1

hide column, 19.1.39

compounds, 19.7

side, 10.3.29

sp3, 10.11.2

by side, 10.3.29

spec, 3.7.2

error, 24.1.19

specialized docking, 14

stereo, 3.6.3.6

specifications, 24.1.5

chain refinement, 18.14

specs, 1

chains, 9.10

faq, 24.1.5

side-by-side, 24.1.19

speed, 6.10.7.2

side-chain optimization, 9.20

sphere, 24.4.11

split, 10.36.1

Calpha, 5.5.3

spreadsheet, 10.20.2

arrange.grid, 5.5.5

square, 24.4.7

backbone, 5.5.3

stability, 9.15, 23.5.3, 23.5.4

heavy atoms, 5.5.3

stack, 9.8.2, 9.8.2.1, 9.21, 9.23.18, 12.7, 14.2.3.7, 24.9.8

multiple, 5.5.4

calculations, 9.23.18

superposition, 10.37, 10.37.1, 10.37.2, 10.37.5, 10.37.6, 23.3.3, 23.8.1

stacking, 5.3.2

surface, 3.7.1, 4.20.5, 5.2.2, 5.2.3, 6.1.6, 6.3, 6.3.3, 6.3.4, 24.2.16, 24.2.37, 24.4.19

standalone hitlist, 12.7.1.4

area, 5.6

standard table, 19.1

area, 5.6.5

standardize, 10.12

surfaces, 5.2, 6.3.1, 6.3.2, 6.10.5

table, 10.12

surrounding, 24.4.11

start, 10.10.2

swissprot, 8.1, 8.5

startup, 24.10.2

sxstrace, 24.1.19

static, 24.4.8

symmetric oligomer, 9.1.3

stereo, 4.20.6, 6.6, 10.3.28, 10.4.2, 24.1, 24.1.6, 24.1.7, 24.1.14

symmetry, 5.4.1, 5.4.3, 23.3.8, 23.3.9

bond, 10.4.2

synthesize, 10.11.7

hardware, 3.6.3.7

synthetic feasibility, 10.11.7

side-by-side, 3.6.3.6

system preferences, 4.20.11

stereohard faq, 24.1.6

tab, 19.1.2, 19.1.21

stereoisomer, 10.20.5

pdb, 3.7.4

stereoisomers, 10.25

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, 18.10, 19, 19.1.6, 19.1.35, 19.1.40, 19.1.45, 19.4, 19.4.1, 19.4.4, 19.4.9, 19.4.11, 19.4.13, 19.4.14, 19.4.15, 19.4.16, 19.4.17, 19.4.18, 19.4.20, 19.7.1, 24.4.19, 24.8.4, 24.8.5, 24.8.7, 24.8.8

stick, 4.20.5

alignment, 19.1.12

stl, 6.7

clone, 19.1.16

stop, 6.10.7.3

color, 19.1.10

store, 3.6.3.19, 6.10.7.4, 24.2.22

column format, 19.1.40

current view, 3.6.3.19

copy, 19.1.36, 19.1.37

faq, 24.2.22

delete, 19.1.17

strain, 5.7.4, 6.12.6.1, 10.17, 10.27, 10.27.2, 12.1.10, 12.7.1.2, 18.4

edit, 19.1.24

strip, 24.4.9

filter, 19.1.43

structure, 5.4.3, 11, 19.6, 23.3, 24.4

find, 19.1.9

analysis, 5.6.12, 23.3.4

replace, 10.3.32

ensemble, 9.23.14

font, 19.1.11

prediction, 9.8

size, 24.2.1

preparation, 9.20

grid, 19.1.5

representation, 6.1

histogram, 19.4.1

smiles, 10.20.4

insert, 19.1.26

structure-based, 12.4

layout, 19.1.5

structures, 10, 10.1

learning, 19.6

style, 4.20.5

mark, 19.1.13

substituent, 10.9.1, 10.9.2, 10.35.2, 18.5.2

row, 19.1.13

substructure, 10.10.4, 10.13, 10.37.1, 10.37.2, 12.10, 24.8.1, 24.9.5

mouse, 19.1.47

template, 18.12.3

navigation, 19.1.4

alerts, 10.13

new column, 19.1.26

sugar conformation, 5.6.12

plot, 19.4

pucker analysis, 5.6.12

print, 19.1.19

puckering, 5.6.12

rename, 19.1.15

ring puckering, 5.6.12

rightclick, 19.1.14

sulfur, 9.11

row height, 24.2.39

superimpose, 3.6.8, 5.5.2, 5.5.6, 10.37.4, 23.3.3, 24.2.5, 24.4.6, 24.4.7, 24.4.8

save, 19.1.3

3D, 5.5.3

selection, 19.1.3

select, 19.1.23

scroll, 19.1.4

setup, 19.1.18

sdf, 10.3.9

sort, 19.1.42

select, 19.1.23

split fragments, 10.3.33

setup, 19.1.18

view, 19.1.5

sort, 3.6.10.4, 10.3.5, 19.1.42

save, 19.1.8

standard, 19.1

zoom translate, 10.3.30

view, 10.3.29

action, 19.1.47

width, 19.1.4

alignment, 19.1.12

tables, 10.31, 19

append, 19.1.43

tag, 4.6.21, 18.5.7, 19.1.46

clone, 19.1.16

tags, 4.6.21

color, 19.1.10

m, 5.6.12

column, 10.3.4, 19.1.26, 19.1.32, 19.1.39

tautomer, 10.24, 24.4.15

columns, 10.3.8

tautomers, 10.24

compare, 10.3.22

temperature, 5.7.5

copy, 10.3.6

template, 9.1.2, 10.4.6, 10.37

cursor, 19.1.47

docking, 24.5.3

delete, 19.1.14, 19.1.17

templates, 10.4.6

display, 24.10.4

terminal, 10.3.28

double.click, 19.1.47

font size, 24.2.1

edit, 10.3.17

tether, 12.8, 18.12.1, 18.12.2

excel, 10.3.10, 19.1.20

text, 4.20.7, 7.6, 7.6.1, 7.6.7, 10.3.28, 10.10.4, 19.4.24, 24.9.6

filter, 10.3.12, 19.1.43

search, 10.5.4

find-replace, 10.3.13

texture, 3.7.6

to screen, 19.1.4

thoroughness, 10.23, 10.37, 24.5.12

font, 19.1.11

three, 10.3.24, 24.8.6

foreground, 24.10.4

threshold, 4.20.5

grid lines, 19.1.4

tier, 4.14

hide, 19.1.39

time, 24.5.11

hyperlink, 10.3.15

machine, 24.1.15

insert, 19.1.33

tissue, 4.16.9

join, 3.6.10.5

racemic, 10.20

label, 10.3.14

tools 3D, 3.6.6

landscape, 19.1.18

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, 19.1.47

plot function, 3.6.9.1

name, 19.1.15

superimpose, 3.6.8

new, 19.1.1

table, 3.6.10

options, 19.1.14

Learn, 3.6.10.1

orientation, 19.1.18

clustering, 3.6.10.3

portrait, 19.1.18

merge, 3.6.10.5

print, 10.3.11, 19.1.4, 19.1.19

predict, 3.6.10.2

read, 19.1.2

tooltip, 19.4.26

rename, 19.1.15

balloons, 19.4.26

right click, 19.1.14

torsion, 6.12.6, 6.12.6.1, 9.23.7, 10.17, 18.5.4, 24.4.16

row, 19.1.33

analysis, 10.16

rows, 3.6.10.7

angles, 6.12, 6.12.6

save, 10.3.9, 19.1.3, 19.1.4, 19.1.21

free strain, 10.17

scale, 19.1.18

scan, 9.23.7, 16

trace, 6.1.10

uniprot, 4.16.5, 8.5

transition.blend, 24.2.31

unique, 10.3.28, 10.33

transitions, 7, 24.2.30

unit, 5.4.3

translate, 4.4, 6, 6.12, 10.3.30

units, 24.5.1

translation, 6.12.3, 8.3.3, 19.4.17

unix, 24.10.2

transparent, 6.3.9.3

unsatisfied hydrogen bonds, 18.3.8

background, 6.15.3

unusual peptide, 4.17

ribbon, 24.2.3

update, 9.8.5

surface, 24.2.37

upload, 21.2

tree, 8.7.8, 10.28.7, 19.7.2, 19.7.3, 19.7.4

use activeicm, 7.12

branch swapping, 8.7.8

user, 10.10.5, 21.5

distance, 10.28.3

defined groups, 18.5.3

edit, 10.28.4

modifiers, 18.5.3

reorder, 10.28.3

user-defined groups, 10.4.5

triplet, 10.4.7

van der waal, 6.8.15

trouble shooting, 24.1.11

variable, 4.20.7, 24.2.8

trouble-shooting, 24.1.12

verbose, 10.23

truncating a mesh object, 24.2.15

large sdf files, 10.1.2

crash qlock, 24.1.13

vicinity, 10.23

tsv, 19.1.21

video, 2, 6.16, 6.16.1, 6.16.2

tut analyze alternative orientations, 23.3.11

view, 3.6.3.19, 7.3.1, 10.3.28, 24.2.22, 24.9.8

occupancy, 23.3.10

animate view, 3.6.3.15

symmetry, 23.3.9

center, 3.6.3.20

multiple receptor, 23.12.1

color background, 3.6.3.18

tut3, 23.5

dock results, 12.7

tut3e, 23.3.12

fog, 3.6.3.5

tut5a, 23.9.1

macroshape, 3.6.3.22

tut5b, 23.9.2

menu, 3.6.3

tut5c, 23.11.1

mesh clip, 6.13.1

tut5e, 23.11.2

perspective, 3.6.3.9

tutorial 2D pharmacophore, 23.6.6

selection level, 3.6.3.3

3D pharmacophore, 23.6.5

mode, 3.6.3.4

chemical clustering, 23.6.3

shadow, 3.6.3.13

search, 23.6.2

sketch accents, 3.6.3.14

molecular documents, 23.2

slide show, 7.3.1

sequence alignment, 23.4

tools, 3.6.3

link, 23.4.2

tree, 19.7.4

load sequence, 23.4.1

undisplay all, 3.6.3.1

sequence conservation, 23.4.3

stach, 9.23.15

tutorials, 23

virtual, 12.5, 12.5.1, 12.5.2, 23.9, 23.11.1

two, 10.3.24, 24.8.6

ligand screening, 17

ubuntu, 24.1.18

screen, 13.1, 13.2

ultra large library, 12.6

screening, 12.4, 12.12

unclip, 6.3.10, 6.13.1

examples, 23.11

undisplay, 4.5, 6.1.7, 24.2.10, 24.2.32

virus, 5.4.3

box shade font, 8.7.7.1

visualize, 10.30

undisplay-all, 3.6.3.1

apf fields, 18.3.11

origin, 6.8.12

chemical space, 10.30

undo, 3.6.2.9, 4.20, 10.4.11, 18.5.5

ligand strain, 18.3.10

redo, 18.5.5

vls, 12.4, 12.5, 12.5.6, 12.5.7.2, 12.7.7.4, 12.9, 12.9.3, 13.1, 15.4, 23.11.2, 24.5.7, 24.5.8, 24.5.24

display, 12.7.7.3

youtube, 2

command line, 12.5.7.2

zoom, 4.4, 6, 6.12, 6.12.4, 10.3.30, 19.4.17

getting started, 12.5.2

τm, 5.6.12

histogram scatter plot, 12.7.7.2

introduction, 12.5.1

preferences, 12.5.4

results, 12.5.8

run, 12.5.6

score, 12.1.9

visualization, 12.7.7.8

results, 12.5.8

volume, 10.4.9

water, 9.23.17, 12.1.8

waters, 9.23.17

wavefront, 3.7.6, 6.3.11, 6.7

weak, 24.4.20

web, 23.2

browser, 3.6.1.12

weight, 10.11, 24.8.7, 24.8.10

weighted, 19.7.1

weights, 9.8.5

width, 19.1.22

window, 4.14

windows, 4.14.1, 10.10.1

wire, 3.7.1, 4.20.5, 6.1.1, 24.2.4, 24.2.21

wireBondSeparation, 4.20.1

working directory, 24.5.23

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, 19.4.21, 24.9.4, 24.9.7

alignment, 8.7.3

excel, 10.2.3

image, 3.6.1.15, 24.1.20

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, 19.1.3

writing a pdb file, 24.4.3

ray, 3.6.5

xi, 6.8.5, 24.2.18

xls, 10.2.3

xlsx, 10.2.3

xml, 21.2

xstick, 6.1.2, 24.2.21

xyz, 24.2.10