F: Sub Index for SYBYL and UNITY Documentation

F-ratio, definition

• Terminology of Multiple Regression and PLS

Factor analysis

algorithm

• Factor Analysis Algorithm

benzene coordinates

• Theoretical Introduction to Factor Analysis

command entry

• Factor Analysis via Command Line

communality

• Factor Analysis Algorithm

dialog

• Factor Analysis via the Menubar

eigenvalues

• Theoretical Introduction to Factor Analysis

graphs

• Graph Analysis Results

eigenvalues

• Graph Analysis Results

loadings

• Graph Analysis Results

original data

• Graph Analysis Results

• Graph Analysis Results

• Graph Analysis Results

scores

• Graph Analysis Results

quartimax rotation

• Factor Rotation

rotation of axes

• Factor Rotation

TAILOR

• TAILOR SET FACTOR

theory

• Theoretical Introduction to Factor Analysis

varimax rotation

• Factor Rotation

Family

column type

• FAMILY Column Type

create new

• Create New Family

technique

• FAMILY Column Type

view

• View Family

FASTA file

format

• Run FUGUE

format

• Common Biopolymer File Formats

reading and writing

• Read and Write PIR and FASTA Files

Fault Tolerance

tps

• Fault Tolerance

Features

• Define Basic Features

acceptor atom

• Acceptor Atom

acceptor on protein

• Protein Acceptor Atom

acceptor site

• Acceptor Site

aligning scale factor

• Define Basic Features

aromatic area

• Aromatic Area

centroid

• Centroid

class definitions

• Specify 3D Queries

coloring

• Special Notes:

donor atom

• Donor Atom

donor on protein

• Protein Donor Atom

donor site

• Donor Site

extension point

• Extension

fragment

• Fragment

hydrophobic area

• Hydrophobic Areas

line

• Line

managing

• Define or Modify Features/Constraints

naming

• Define Basic Features

negative center

• Negative Center

on protein

• Protein Negative Center

normal

• Normal

OR

• OR Feature

plane

• Plane

positive N

• Positive N

on protein

• Protein Positive N

steric feature

• Steric Feature

tetrahedral

• Tetrahedral

edit or view

• View or Edit Features

requirements

• Specify Input Model Criteria

identified

• Prepare Structures for GASP

center of mass

• Center of Mass

centroid

• Centroid

extension point

• Extension Point

line

• Line

normal

• Normal

plane

• Plane

SYBYL object definition

• Definitions of SYBYL Objects

UNITY

• UNITY Query Features

acceptor atom

• Acceptor Atom

acceptor on protein

• Protein Acceptor Atom

acceptor site

• Acceptor Site

aligning scale factor

• Define Basic Features

aromatic area

• Aromatic Area

centroid

• Centroid

class definitions

• Specify 3D Queries

coloring

• Special Notes:

donor atom

• Donor Atom

donor on protein

• Protein Donor Atom

donor site

• Donor Site

extension point

• Extension

fragment

• Fragment

hydrophobic area

• Hydrophobic Areas

line

• Fragment

naming

• Define Basic Features

negative center

• Negative Center

on protein

• Protein Negative Center

normal

• Normal

OR

• OR Feature

plane

• Plane

positive N

• Positive N

on protein

• Protein Positive N

steric feature

• Steric Feature

tetrahedral

• Tetrahedral

FETCH_SLN_OPS

• FETCH_SLN_OPS

FF_SETUP

• Setup an Energy Calculation via Command Line, Without Executing the Job

Field

lines

• Working with Cones & Field Lines Interactively

interaction

• Working with Cones & Field Lines Interactively

syb3dbserver command

• Open a Database

CoMFA

• CoMFA Fields

descriptions

• CoMSIA Field Descriptions

general meaning

• Building Spreadsheet for CoMFA

graph

• Examination and Use of CoMFA Results

retrieve

• Examination and Use of CoMFA Results

type

• Examination and Use of CoMFA Results

Field fit

• Field Fit

in CoMFA

• The QSAR Table

in force field options

• Calculate Energy via Command Line

template

• Manage CoMFA Alignments in SYBYL

theory

• Field Fitting

use in QSAR or minimization

• Use in QSAR or Minimization

TAILOR

• TAILOR SET FIELD_FIT

File formats

2D coordinate generation

• Generate Coordinates

aromaticity normalization

• Normalize Aromaticity

hitlist

• The Hitlist File

SLN ID range rules

• SLN ID Range Rules File

standardization

• Standardize Structures

tuplets.cfg

• tuplets.cfg

.box file

• Generate/Save a Lattice

SybylHardcopy.lst

• Printing the SYBYL Display

.syb

• The .syb File Format

AMPAC/MOPAC output file

• The .syb File Format

quantum chemistry

• The .syb File Format

Tailor

• Save Tailor Variables

.acnt

• ASCII Contour File

.mol file

• Mol File Format

.mol2 file

• Mol2 File Format

alternate atom type

• @<TRIPOS>ALT_TYPE

anchor atom

• @<TRIPOS>ANCHOR_ATOM

angle constraint

• @<TRIPOS>FFCON_ANGLE

associated annotation

• @<TRIPOS>ASSOCIATED_ANNOTATION

atom

• @<TRIPOS>ATOM

bond

• @<TRIPOS>BOND

center of mass

• @<TRIPOS>CENTER_OF_MASS

centroid

• @<TRIPOS>CENTROID

crysin

• @<TRIPOS>CRYSIN

data file

• @<TRIPOS>DATA_FILE

dictionary

• @<TRIPOS>DICT

distance constraint

• @<TRIPOS>FFCON_DIST

example

• Sample Mol2 File

extension point

• @<TRIPOS>EXTENSION_POINT

force field periodic boundary conditions

• @<TRIPOS>FF_PBC

glossary

• Glossary and Format Restrictions

line

• @<TRIPOS>LINE

molecule

• @<TRIPOS>MOLECULE

multifit constraint

• @<TRIPOS>FFCON_MULTI

normal

• @<TRIPOS>NORMAL

plane

• @<TRIPOS>LSPLANE

QSAR alignment rule

• @<TRIPOS>QSAR_ALIGN_RULE

range constraint

• @<TRIPOS>FFCON_RANGE

ring closure

• @<TRIPOS>RING_CLOSURE

rotatable bond

• @<TRIPOS>ROTATABLE_BOND

search distance constraint

• @<TRIPOS>SEARCH_DIST

search options

• @<TRIPOS>SEARCH_OPTS

set

• @<TRIPOS>SET

special characters

• Glossary and Format Restrictions

substructure

• @<TRIPOS>SUBSTRUCTURE

torsion constraint

• @<TRIPOS>FFCON_TORSION

UNITY atom attribute

• @<TRIPOS>UNITY_ATOM_ATTR

UNITY bond attribute

• @<TRIPOS>UNITY_BOND_ATTR

UNITY feature

• @<TRIPOS>U_FEAT

contour file

• ASCII Contour File

Quick Find list

• Documented File Formats

.demo file

• Play Recorded Session

.loop file

• Biopolymer Loop Files

.pir file

• Common Biopolymer File Formats

Biopolymer files

• Biopolymer Loop Files

FASTA file

• Common Biopolymer File Formats

loop modeling

• Biopolymer Loop Files

protein homology matrix

• Protein Homology Matrix Files

CRYSIN

• CRYSIN File Formats

File Name Extensions

.core, .spl

• TAKE vs. UIMS LOAD

File selection dialog

• Open (Read) Molecule File via the Menubar

Files

application

• APPLICATION File

FASTA format

• Run FUGUE

network access

• User and Password Information Locations

edit

• View and Edit Text Files in SYBYL

reading/writing

MDL Mol file

• Manage Input/Output Formats

SD file

• Manage Input/Output Formats

SLN

• Manage Input/Output Formats

Files created

binary bitmaps

• Tuplet Creation

hitlist manager

.uhlm.properties

• Set Display Preferences

• Combine Hitlists

recently opened files

• Open and Close

Tuplets

• Create/Open Projects

CScore

• CScore Subset Extraction Tool

• Select the CScore Output Formats

DISCOtech

• Introduction to DISCOtech

CDF file

• FlexX-Pharm Constraints

Docking

• The Docking Files

EDF file

• Define the FlexE EDF File

FlexE

• The Docking Files

FlexX

• FlexX Details

• The Docking Files

RDF file

• Access FlexX

SFXC file

• Access Surflex-Dock

Surflex-Dock

• Surflex-Dock Details

• The Docking Files

ANNEAL

• Minimize a Subset of Residues

DYNAMICS

• Dynamics in SYBYL

table

• Options for Analyzing Dynamics Results

LATTICE

• Generate/Save a Lattice

MAXIMIN2

• Minimize Energy in SYBYL

MULTIFIT

• Minimize and Fit Multiple Structures

Torsional minimizer

• Torsion Minimization

FUGUE

• View Family

JOY

• joy

CONTOUR

• CONTOUR

DOTS

• DOTS

HARDCOPY

• HARDCOPY

MVOLUME

• MVOLUME

POTENTIAL

• POTENTIAL

Legion

• Files Created by Legion

installed column type

• Install an SPL Column Type via the Keyboard

Molecular Spreadsheet

• Export Data from a Spreadsheet or Table to a File

SPL

• Install an SPL Column Type via the Keyboard

TABLE

• Save a Molecular Spreadsheet or Table

ORCHESTRAR

• ORCHESTRAR Input and Output Files

SUPERIMPOSE

• Superimpose Atoms

QSAR

analysis

• Perform Analysis

• Repeat QSAR Analysis

• Factor Analysis via Command Line

• Hierarchical Clustering via Command Line

• Access RNN in SYBYL

• Jarvis-Patrick Clustering via Command Line

• Access PLS via Command Line

• Access SIMCA via Command Line

CoMFA

field

• Calculate Electrostatic/Steric Field

AMPAC

• AMPAC Files

MO plots

• MO PLOTS

MOPAC

• Access MOPAC in SYBYL

grid searching

• Grid Search

multisearch

• Search Multiple Molecules

random search

• Random Conformational Search

systematic search

• Systematic Conformational Search

Selector

• Files Created by Selector

FlexS

• Access FlexS in SYBYL

Surflex-Sim

• Access Surflex-Sim in SYBYL

Topomer Search

• Files Created by Topomer Search

Tailor

• Save Tailor Variables

Netbatch

• Summary of the Netbatch Procedure

CAPTURE

• Record Output from a Single Command

COLLECT

• Record Session Commands

DATABASE

• Open a New, Empty Database

WRITE_FILE2

• Save Database Molecules to Mol2 Files

Mol2

• Save (Write) Molecule File via the Menubar

SD files

• Manage Input/Output Formats

BIOPOLYMER

CONSTRUCT BACKBONE

• Build C-alpha to Backbone

LOOP

• Introduction to Loop Searches

LOOP ANALYZE

• Analyze Search Results

PREDICT

• Predict Secondary Structure

biopolymer trace

• Biopolymer Chain Trace and Backbone Display

CombiFlexX

• The CombiFlexX Files

CRYSIN

SAVE

• Save Entire Definition of Molecule to ASCII File

SYMMETRY SAVE

• Specify Symmetry Information for Molecule

Fill valences

Fill valences

• Atoms

Fill valences

• Valence Filling

Filter

operator

• Filter Operator

property data

• Non-Structure Data Importing

symmetries and geometric inconsistencies

• Postprocessing

Filters

salts

• Filtering Salts

FILTER_OPS

• FILTER_OPS

FILTER_TOOLS

• FILTER_TOOLS

Final Optimization and Output Options

Confort

• Task

Find duplicates

• PKG_FIND_DUPS

Find hits

• Examine Hitlist

Findconf built-in set

• Built-in Sets

FindLicenseFile

• Managing Licenses Outside of SYBYL

Fingerprint

2D definition

• Description of Screen Files

apply, O/S utility

• Create Screens via O/S Utilities

create, O/S utility

• Create Screens via O/S Utilities

creation tutorial

• Create Fingerprints

fragment based

• Description of Screen Files

fragment length based

• Description of Screen Files

vector

• Hypothesis Creation

vector sum

• Hypothesis Creation

descriptors in Selector

• Fingerprint Descriptors

2D definition

• Screen Rules

API package

• FPRINT_OPS

fragment based

• Screen Files

fragment length based

• Screen Files

indexing

• Create Fingerprint Domain Index

operators

• Fingerprint Operators

parallel calculation

• Parallel Fingerprint Calculation

replace rules

• Replace Fingerprint Rules

Fingerprints

atom-pair

• FPRINT_OPS

generic

• FPRINT_OPS

sparse

• FPRINT_OPS

Fitness

score

• Fitness Score

Fitness function

• Fitness Function

Fitting

atoms

• Fit Atoms

field fit

• Field Fit

flexible fit

• Minimize and Fit Multiple Structures

least squares fit

• Fit Atoms

match atoms

• Match Atoms

multiple molecules

• Minimize and Fit Multiple Structures

superimpose atoms

• Superimpose Atoms

tutorial

• Conformational Comparison Tutorial

biopolymers

• Fit Monomers

conformers to the average

• RMS Fits of Conformers

Fixing

amide chains

• Fix Sidechain Amides

prolines

• Fix Prolines

sidechains

• Scan Sidechain Torsions

terminal residues

• Fix End Groups

FlexE

• FlexE

EDF file

• Define the FlexE EDF File

ensemble description file (EDF)

• Define the FlexE EDF File

files created

• The Docking Files

heteroatoms and alternate groups

• Define Heteroatoms and Alternate Groups

null atom

• Define Heteroatoms and Alternate Groups

protein preparation

• FlexE

sequence equivalence

• FlexE Equivalence Sequences

setting transfer

• Transfer FlexE Settings

theory

• FlexE: Docking into Protein Ensembles

tutorial

• Docking with FlexE

Flexibility

theory

• Flexibility (FX)

Flexible alignment

individually to a template

• Flexibly Align Ligands Individually to a Template

to each other and a template

• Flexibly Align Ligands to Each Other Using a Template

to other ligands

• General Instructions for Common Tasks

Flexible search

amide bond planarity tolerance

• Control Performance of Flexible Searching

controlling performance

• Control Performance of Flexible Searching

environment variables

TA_AMIDE_TOLERANCE

• Control Performance of Flexible Searching

TA_MAX_TIME_PER_STRUCT

• Control Performance of Flexible Searching

UNITY_FLEX_ADJUST

• Control Performance of Flexible Searching

UNITY_FLEX_MODE

• Control Performance of Flexible Searching

UNITY_MAX_ITER

• Control Performance of Flexible Searching

UNITY_MAX_RESETCOUNT

• Control Performance of Flexible Searching

UNITY_MAX_STEPCOUNT

• Control Performance of Flexible Searching

UNITY_MAXROTBONDS

• Control Performance of Flexible Searching

UNITY_MIN_GRADIENT

• Control Performance of Flexible Searching

UNITY_STATIC_FIRST

• Control Performance of Flexible Searching

UNITY_TARGET_FACTOR

• Control Performance of Flexible Searching

iterations for vdw check

• Control Performance of Flexible Searching

number of rotatable bonds

• Control Performance of Flexible Searching

output columns

• Flexible 3D Searches

overview

• Flexible 3D Searches

query format

• Flex Queries

ring flexing

• Control Performance of Flexible Searching

save query

• Set and Save Flexible Search Options with Query

search gradient

• Control Performance of Flexible Searching

search mode

• Control Performance of Flexible Searching

search time per structure

• Control Performance of Flexible Searching

setting number of starting conformations

• Control Performance of Flexible Searching

syb3dbserver

• General Setup of a Search via syb3dbserver Command Line

UNITY FLEXSEARCH

• Specify Flexible Search Options via SYBYL Command Line

Flexible superposition

flowchart

• Flexible Superposition

flexlmrc file

• The .flexlmrc File

FlexS

advanced parameters

• Advanced FlexS Parameters

alignment details

example

• Set the Conditions for the FlexS Job

command line

• Run FlexS from the Command Line

configuration files

• Access FlexS in SYBYL

configuring for use with SYBYL

• FlexS Expert's Corner

Confort

• Access FlexS in SYBYL

details

• Access FlexS in SYBYL

graphical user interface

• Using the Similarity Suite

introduction

• Introduction to the Similarity Suite

license requirements

• Introduction to the Similarity Suite

output directory

• FlexS Job Output Directory

output files

• Access FlexS in SYBYL

PVM, using in SYBYL

• Batch Distribution

results browser

• Analyze Results

ring flexibility

• Access FlexS in SYBYL

runtime parameters

• FlexS Runtime Parameters

SYBYL interface

• Access FlexS in SYBYL

theory

• FlexS Theory

transform details

• Transform Details

tutorials

• FlexS Tutorial

FlexX

active site creation

• Define the Active Site

advanced parameters

• Advanced FlexX Parameters

alternate coordinate location

• Customize the FlexX RDF File

building the ligand in the active site

• The FlexX Method

CDF file

• FlexX-Pharm Constraints

columns in the results spreadsheet

• Columns in the FlexX Results Spreadsheet

command line

• Run FlexX from the Command Line

configuration files

• FlexX Details

configuring for use with SYBYL

• Configure FlexX for Use with the SYBYL Interface

Confort

• FlexX Details

details

• FlexX Details

dialogs

• Access FlexX

docking with FlexE constraints

• Docking with FlexE

docking with FlexX-Pharm constraints

• Docking with FlexX-Pharm Constraints

files created

• The Docking Files

flexibility

• Conformational Flexibility in FlexX

graphical user interface

• Using the Docking Suite

grid computing

• Grid Computing

heteroatoms

• Customize the FlexX RDF File

input from SiteID

• Create SiteID Table

introduction

• Introduction to the Docking Suite

license requirements

• Introduction to the Docking Suite

output files

• FlexX Details

placing the base fragment in the model

• The FlexX Method

PVM, using in SYBYL

• Parallel Virtual Machine - PVM

RDF file

• Access FlexX

RDF file customizing

• Customize the FlexX RDF File

references

• Suggested Reading about the FlexX Suite

results

• FlexX Results

results browser

• Analyze Docking Results

ring flexibility

• FlexX Details

ring systems

• Conformational Flexibility in FlexX

runtime parameters

• FlexX Runtime Parameters

scoring protein-ligand interactions

• Scoring Protein-Ligand Interactions with FlexX

selecting the base fragment

• The FlexX Method

single molecule docking

• Single Molecule Docking with FlexX

suggested reading

• Suggested Reading about the FlexX Suite

template manager

• Customize the FlexX RDF File

theory

• The FlexX Suite

torsion manager

• Customize the FlexX RDF File

transform details

• Transform Details

tutorials

• Multiple Molecule Docking with FlexX

FlexX-Pharm

constraint definitions

• The FlexX-Pharm Constraints

constraint file (CDF)

• FlexX-Pharm Constraints

CScore extraction

• CScore Subset Extraction Tool

interaction constraints

• Define FlexX-Pharm Interaction Constraint

logical expression

• FlexX-Pharm Constraints

spatial constraints

• Define FlexX-Pharm Spatial Constraint

tutorial

• Docking with FlexX-Pharm Constraints

FlexXc

customizing

• Customize the FlexXc Job

files created

• The CombiFlexX Files

setting up

• Prepare a CombiFlexX Job

theory

• The FlexXc Approach

tutorial

• FlexXc Tutorial

Flowchart

flexible superposition

• Flexible Superposition

rigid superposition

• Rigid Superposition

Font

change

• Text

changing in hitlist manager

• Set Display Preferences

Force field

AMBER4.1 FF95

• AMBER4.1_FF95 Force Field

AMBER7_FF02

• AMBER7_FF02 Force Field

AMBER7_FF99

• AMBER7_FF99 Force Field

Kollman

• Kollman Force Field

parameters

Kollman

• Parameter Files

Tripos

• Parameter Files

parameters

TAILOR

• TAILOR SET FORCE_FIELD

Tripos

• Tripos Force Field

Kollman

• The Kollman Force Field

Fork process, syb3dbserver

• Send Input To Server

Format

aromaticity normalization

• Aromatic Normalization

hitlist

• Appendix B: Hitlist Format

FPRINT_INDEX_TYPE

• Create Fingerprint Domain Index

FPRINT_OPS

• FPRINT_OPS

Fractional coordinates

• CRYSIN

FRAGDB, CODA fragment database

• CODA

Fragment

• SLN Language

Fragment

• SLN Language

based fingerprints

• Description of Screen Files

feature

• Fragment

length based fingerprints

• Description of Screen Files

length in screens

• Description of Screen Files

generation

• Fragment Generation

listing

• HQSAR Menubar

• HQSAR SHOW_FRAGMENTS

FRAGMENT

• Load Fragments

library

• Fragment Library Structure and Contents

access from sketcher

• Sketcher Menu Items

structure and contents

• Fragment Library Structure and Contents

based fingerprints

• Screen Files

count

SLN_OPS method

• SLN_OPS

SLN_T method

• REG_T Type

length based fingerprints

• Screen Files

length in screens

• Screen Files

list

• SLN_OPS

feature

• Fragment

Fragment SLN, definition

• Introduction to Legion

Fragment Training Molecules dialog

• Fragment the Training Molecules

FREAD

command

examples

• CODA

format

• CODA

Free energy

solvation, column type

• Append Structural Columns

transfer, column type

• Append Structural Columns

Freeze

Freeze

• FREEZE

coordinates before merging

• Merge Atoms and Associated Data Structures

FREE_SEARCH_LICENSE

• Control Engines, Queueing, and Searches

FSLN

creating and reusing

• dbfsln

FSLN, definition

• Introduction to Legion

FUGUE

analyzing results

• Analyze FUGUE Results

bibliography

• FUGUE Recommended Reading

command line

• FUGUE Command Line

creating a family

• Create New Family

expert's corner

• FUGUE Expert's Corner

gap penalties

• Standard Sequence Alignment Scoring

graphical user interface

• FUGUE Graphical User Interface

introduction

• Introduction to FUGUE

output files

• View Family

running

• Run FUGUE

standard sequence alignment

• Standard Sequence Alignment Scoring

structural profiles

• Structural Profiles

theory

• FUGUE Theory

tutorial

• FUGUE Tutorial

view simple model

• View Simple Model

viewing a family

• View Family

workflow

• FUGUE Workflow

fugueali

• Automatic Selection of Alignment Algorithms

• fugueali

fugueprf

• fugueprf

fugueseq

• Automatic Selection of Alignment Algorithms

• fugueseq

fugue_pir_compat.sh

• fugue_pir_compat.sh

Full screen mode

• STATIC

Function based index

• Function Based Indexes

Function keys

Function keys

• Keyboard Function Keys

Function keys

• X Window System Resources

Functional data column type

• FUNCTIONAL_DATA Column Type

Functions

for SLNs

• SLN_OPS

UDC_IMPORT

• Server Side Import

FUSE

TAILOR

• TAILOR SET FUSE

Fuse ring

• Combine (Fuse) Two Molecules From Different Molecule Areas

monitor distances

• TAILOR SET MONITOR

tutorial

• Ring Fusion Tutorial

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Numerics A B C D E F G H I J K L M N O P Q R S Symbols T U V W X Z

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Links to individual Index Files:
• BASICS
• BIO
• CFX
• CONCORD
• CONFORT
• CRYSTAL
• CSCORE
• DISCOTECH
• DISTILL
• DOCKING
• DVS ADDONS
• FORCE FIELD
• FUGUE
• GALAHAD
• GASP
• GENSURF
• GRAPHICS
• HQSAR
• INSTALL_ADMIN
• LEGION
• MOLCAD
• MOLCADPLUS
• MSS
• ORCH
• OVERLAY
• PROTABLE
• QSAR
• QUANTUM
• RACHEL
• SEARCH
• SELECTOR
• SIMILARITY
• SITEID
• SLN
• SLN_AUSPYX
• SPL
• STEREOPLEX
• TAILOR
• TOOLKIT
• TOPCOMFA
• TUPLETS
• UNIFIED_BOOK
• UNITY

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Copyright © 2007, Tripos, Inc. All rights reserverd.