THINK Index

2D

THINK User Guide: 1 Introduction; 2 Reading and Saving Molecules; 3.2 Editing Molecules; 4.1 Input Molecules; 4.2 Viewing Molecules; 4.2.1 2D Display Mode; 4.2.2 3D Display Mode; 4.2.4 Annotation and Labelling; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.6 View Atom Data; 5.1 Input Molecule(s); 6.1 Input Molecules; 8 Searching; 8.2 Search Options; 8.3 Search Results; 8.4 Perform Search; 8.5 View Search Results; 12.4 Select Data to be Analysed; 12.5 Analyse Data; 13.1 Input Molecules; 14 De Novo Molecule Generation; 14.1 Input Molecules; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.3 R-group Search Output; 15.4 R-group Search; 15.5 Enumeration Inputs
THINK Theory Manual: 2 Reading and Saving Files; 2.2.2 Extensions; 3.1 2D Calculations; 8 Molecule Searching; 8.4 3D Searching; 8.5 Site Searching; A.1 Atom Types
THINK Release Notes: CUSTOM EXTENT; 2D Draw enhancements; KNIME Node Speed; Bridged rings; 2D Edit; 3D De Novo; Implicit Hydrogens; KNIME; SD files without hydrogens; Bug fixes; Saving Pharmacophore Coordinates; Bug fixes

3D

THINK User Guide: 1 Introduction; 1.1 User Interface; 2 Reading and Saving Molecules; 3.2 Editing Molecules; 4 Visualisation; 4.1 Input Molecules; 4.2 Viewing Molecules; 4.2.2 3D Display Mode; 4.2.3 3D Manipulation; 4.2.4 Annotation and Labelling; 4.4 Molecular Properties; 4.5 View Diversity; 4.6 View Atom Data; 5 Conformer Generation; 5.1 Input Molecule(s); 5.5 Generate Conformers; 6 Pharmacophores; 6.1 Input Molecules; 6.4 Calculate Pharmacophores; 7.1 Molecule and Pharmacophore Inputs; 8 Searching; 8.1 Query Molecule Input; 8.2 Search Options; 8.3 Search Results; 8.4 Perform Search; 8.5 View Search Results; 9.1 Read Molecules; 9.3 Calculate Map; 10.3 Docking Options; 10.4 Search Results; 10.5 View Docking Results; 11.5 Select Plot Style (1,2); 13.1 Input Molecules; 14 De Novo Molecule Generation; 14.1 Input Molecules; 14.2 Set Molecule Creation Options; 15.5 Enumeration Inputs
THINK Theory Manual: 2 Reading and Saving Files; 2.2.2 Extensions; 2.3 PDB Format; 2.5 Parameter Files; 3.1.2 Volume and Surface Area; 3.2 3D Calculations; 4 Conformer Generation; 4.1 Rotational Bonds; 4.2 Conformer Generation; 7.2 Fuzzy Pharmacophores; 8 Molecule Searching; 8.4 3D Searching; 8.5 Site Searching; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; Appendix B Pharmacophore File Format; C.2 Constants; Appendix D ITRACE Values; 1.4 THINK Clients; 5 Creating Jobs and Analysing Results
THINK Release Notes: CUSTOM EXTENT; THINK v2.00a; De Novo for FBDD; Enhancements to Pharmacophore and 3D Searching; De Novo; Orientate; Superimpose; Atom selection; Bridged rings; KNIME; 3D De Novo; Scroll Bar; SD files without hydrogens; KNIME related changes; Pharmacophore Profiling Performance; Ligand Query Dialog; Side-Chain motion; Map Display; Active Volume Search Constraints; Minor Graphics Enhancements

acceptor

THINK User Guide: 4.4 Molecular Properties; 10 Docking; 12.4 Select Data to be Analysed
THINK Theory Manual: 3.1.1 Counters; 7.1 Centre Types; 9.1 Complementary Centres; 9.5.4 Acid and Base Weighting; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; A.1 Atom Types; Appendix B Pharmacophore File Format

acid

THINK User Guide: 4.4 Molecular Properties; 6.2 Set Pharmacophore Options; 15.1 R-group Search Input
THINK Theory Manual: 2.3 PDB Format; 2.3.1 Key Features; 2.3.4 Limitations; 2.4 Enumeration; 2.4.3 Peptide Chains; 7.1 Centre Types; 8.5 Site Searching; 9.5 Centre Selection (Weighting); 9.5.2 Pharmacophore Score; 9.5.4 Acid and Base Weighting; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; A.1 Atom Types; Appendix B Pharmacophore File Format; C.2 Constants

activity field

THINK User Guide: 2.2 Saving Molecules; 4.4 Molecular Properties; 12.2 Select Activity Field; 12.3 Set Activity Options; 12.5 Analyse Data
THINK Theory Manual: 5 Data Analysis; 5.1 Key Features; 6.2 Application of Earlier Results
THINK Release Notes: Activity Dialog; Ligand Query Dialog

alpha

THINK User Guide: 1.4 Identifying Molecules and Atoms; 1.5.1 Symbols and Operators; 5.3 Set Bond and Ring Increments
THINK Theory Manual: 4.1 Rotational Bonds; C.2 Constants; 1.2 THINK Jobs

amide

THINK User Guide: 5.3 Set Bond and Ring Increments; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.5 Enumeration Inputs
THINK Theory Manual: 2.4 Enumeration; 2.4.2 Coreless Libraries; 4.1 Rotational Bonds; C.2 Constants

area

THINK User Guide: 4 Visualisation; 4.4 Molecular Properties; 5 Conformer Generation; 6 Pharmacophores; 8 Searching; 9 Maps; 10.3 Docking Options; 11 Property Diversity; 12 Data Analysis; 12.4 Select Data to be Analysed; 13 Clustering; 14 De Novo Molecule Generation; 15 Combinatorial Chemistry
THINK Theory Manual: 3.1.2 Volume and Surface Area; 3.1.3 Partial Surface Areas; 5.1 Key Features; 8.5 Site Searching; 9.6.3 Check Pharmacophores and Conformers; C.2 Constants; Appendix D ITRACE Values
THINK Release Notes: CUSTOM EXTENT; 3D De Novo; Pharmacophore volume and area; Active Volume Search Constraints

atom name

THINK User Guide: 1.4 Identifying Molecules and Atoms; 4.2.4 Annotation and Labelling; 15.2 R-group Search Options

atom specification

THINK User Guide: 1.4 Identifying Molecules and Atoms
THINK Release Notes: Protein Sites

base

THINK commands: WRITE
THINK User Guide: 4.4 Molecular Properties; 6.2 Set Pharmacophore Options; 15.7 Enumeration Results
THINK Theory Manual: 2.1.1 Key Features; 2.2.2 Extensions; 7.1 Centre Types; 8.5 Site Searching; 9.1 Complementary Centres; 9.5 Centre Selection (Weighting); 9.5.2 Pharmacophore Score; 9.5.4 Acid and Base Weighting; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; A.1 Atom Types; Appendix B Pharmacophore File Format; C.2 Constants; Appendix D ITRACE Values; 2.5 Starting the Server and Clients; 6 Trouble Shooting
THINK Release Notes: Bug fixes

bin

THINK User Guide: 6 Pharmacophores; 6.2 Set Pharmacophore Options
THINK Theory Manual: 7.2 Fuzzy Pharmacophores; Appendix B Pharmacophore File Format; C.3 Flags
THINK Release Notes: Bug fixes; Active Volume Search Constraints

bond order

THINK User Guide: 2 Reading and Saving Molecules; 3.2 Editing Molecules; 8 Searching
THINK Theory Manual: 2.3.4 Limitations; A.2 Bond Parameters; A.4 Ring Coordinates; A.5 Ring Torsion Angles
THINK Release Notes: Residue Connectivity

build

THINK User Guide: 3.2 Editing Molecules; 15.1 R-group Search Input
THINK Theory Manual: Appendix D ITRACE Values; 5 Creating Jobs and Analysing Results

CALCULATE

THINK commands: ELSE
THINK User Guide: 9.3 Calculate Map
THINK Release Notes: Cavity Maps; Map Display; Active Volume Search Constraints

CALL

THINK commands: LIST
THINK User Guide: 1.3 Log Files; 1.5 Command Scripts and Symbols; 1.5.2 Script Arguments; 6 Trouble Shooting

centres

THINK commands: LABEL
THINK User Guide: 4.2.4 Annotation and Labelling; 4.4 Molecular Properties; 4.5 View Diversity; 6 Pharmacophores; 6.1 Input Molecules; 6.2 Set Pharmacophore Options; 7 DiverseSets and FocusedSets; 7.1 Molecule and Pharmacophore Inputs; 7.2 Pharmacophore Options; 8 Searching; 10 Docking; 10.1 Creating Site Queries; 10.3 Docking Options; 11 Property Diversity; 11.3 Set Calculation Options (1); 11.5 Select Plot Style (1,2); 11.7 Calculate Diversity (1,2); 12.4 Select Data to be Analysed; 14.2 Set Molecule Creation Options
THINK Theory Manual: 3.1.1 Counters; 5 Data Analysis; 7 Pharmacophores; 7.2 Fuzzy Pharmacophores; 8.5 Site Searching; 9.1 Complementary Centres; 9.2 Existing Ligand-Protein Complex; 9.5 Centre Selection (Weighting); 9.5.1 Required Groups; 9.5.3 Distance Weightings; 9.6.1 Visual Inspection; 9.6.2 Check Site Points; 9.6.3 Check Pharmacophores and Conformers; Appendix B Pharmacophore File Format; C.3 Flags
THINK Release Notes: Enhancements to Pharmacophore and 3D Searching; Lipophilic centres; Lipophilic centres; Centre Positions; KNIME related changes; Bug fixes

CHECK

THINK commands: GOTO

chiral

THINK User Guide: 4.4 Molecular Properties
THINK Theory Manual: 2.2.2 Extensions
THINK Release Notes: 3D Coordinate Generator

CLOSE

THINK commands: CLOSE
THINK User Guide: 2.1 Reading Molecules

complementary centres, see centres

conformer

THINK User Guide: 1 Introduction; 2.2 Saving Molecules; 4 Visualisation; 4.2 Viewing Molecules; 4.4 Molecular Properties; 5 Conformer Generation; 5.1 Input Molecule(s); 5.2 Set Search Mode; 5.3 Set Bond and Ring Increments; 5.5 Generate Conformers; 6 Pharmacophores; 6.2 Set Pharmacophore Options; 6.3 Set Conformer Options; 7 DiverseSets and FocusedSets; 7.3 Subset Calculation; 8 Searching; 8.4 Perform Search; 9 Maps; 9.2 Align Molecules; 9.4 Display Map and Molecules; 10 Docking; 10.3 Docking Options; 11 Property Diversity; 12 Data Analysis; 13 Clustering; 14 De Novo Molecule Generation; 14.2 Set Molecule Creation Options; 15 Combinatorial Chemistry
THINK Theory Manual: 1 Introduction; 4 Conformer Generation; 4.1 Rotational Bonds; 4.2 Conformer Generation; 7 Pharmacophores; 7.4 Pharmacophore Files; 8.4 3D Searching; 8.5 Site Searching; 9.6.3 Check Pharmacophores and Conformers; Appendix B Pharmacophore File Format; C.2 Constants; C.3 Flags; 2.4 Customise "screen.srt"; 5 Creating Jobs and Analysing Results
THINK Release Notes: De Novo for FBDD; Enumeration for FBDD; Enhancements to Pharmacophore and 3D Searching; 3D De Novo; Ligand Query Dialog; Conformational Generation; Active Volume Search Constraints; Molecular Mechanics; Pharmacophore Population Profiles

conjugated

THINK User Guide: 5.3 Set Bond and Ring Increments; 6.3 Set Conformer Options
THINK Theory Manual: 3.1.4 Flexibility; 4.1 Rotational Bonds; 9.6.3 Check Pharmacophores and Conformers; A.1 Atom Types; C.2 Constants
THINK Release Notes: Molecular Mechanics

connection

THINK User Guide: 1.1 User Interface; 2 Reading and Saving Molecules; 3.2 Editing Molecules; 4.2.1 2D Display Mode; 8 Searching; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.5 Enumeration Inputs; 15.7 Enumeration Results
THINK Theory Manual: 2 Reading and Saving Files; 2.1 SMILES; 2.1.2 Extensions; 2.2.1 Key Features; 2.3.1 Key Features; 2.3.4 Limitations; 2.4 Enumeration; 2.4.1 Core-based Libraries; 2.4.3 Peptide Chains; 3.1.5 Lipophilicity; 3.3 User-Defined Properties; 8.3 R-group Searching; 8.4 3D Searching; 9.1 Complementary Centres
THINK Release Notes: Duplicate Atoms in PDB files; 3D De Novo; Residue Connectivity; Reading PDB files

contact

THINK User Guide: 4.2 Viewing Molecules; 4.2.4 Annotation and Labelling; 4.4 Molecular Properties; 5 Conformer Generation; 5.2 Set Search Mode; 5.4 Set Contacts Check; 6.3 Set Conformer Options; 8.2 Search Options; 12.4 Select Data to be Analysed; 14.2 Set Molecule Creation Options
THINK Theory Manual: 1 Introduction; 3.2.1 CPK Contacts; 3.2.2 VdW Contacts; 4.2 Conformer Generation; 4.3 Contacts Check; 8.5 Site Searching; 9.2 Existing Ligand-Protein Complex; 9.5.3 Distance Weightings; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; C.3 Flags
THINK Release Notes: Inter and Intra contact colouring; De Novo for FBDD; Enumeration for FBDD; Bug fixes

CPK, see radius

CUSTOMISE

THINK commands: EXIT
THINK User Guide: 2.2 Saving Molecules; 4.2.4 Annotation and Labelling; 4.3 Fingerprint Keys; 5 Conformer Generation; 5.2 Set Search Mode; 5.3 Set Bond and Ring Increments; 5.4 Set Contacts Check; 6.2 Set Pharmacophore Options; 6.3 Set Conformer Options; 8.2 Search Options; 9.3 Calculate Map; 10.3 Docking Options; 15.6 Enumeration Options
THINK Theory Manual: 2.2.1 Key Features; 4.1 Rotational Bonds; 4.2 Conformer Generation; 7.2 Fuzzy Pharmacophores; 8.4 3D Searching; 8.5 Site Searching; 9.5.2 Pharmacophore Score; 9.6.1 Visual Inspection; 2.4 Customise "screen.srt"
THINK Release Notes: Activity Dialog; Saving Pharmacophore Coordinates; Scoring functions; Conformational Generation; Pharmacophore Population Profiles

DELETE

THINK commands: END
THINK User Guide: 3.2 Editing Molecules; 3.3 Deleting Molecules; 15.5 Enumeration Inputs; 1.2 THINK Jobs
THINK Release Notes: Map Display

DISPLAY

THINK commands: DISPLAY
THINK User Guide: 4 Visualisation; 4.2 Viewing Molecules; 4.2.1 2D Display Mode; 4.2.2 3D Display Mode; 4.2.4 Annotation and Labelling; 4.3 Fingerprint Keys; 4.5 View Diversity; 5.5 Generate Conformers; 8 Searching; 8.5 View Search Results; 9.3 Calculate Map; 10.5 View Docking Results; 11 Property Diversity; 11.5 Select Plot Style (1,2); 11.6 Define Activity-Based Colour-Coding (2); 11.7 Calculate Diversity (1,2); 12.6 Apply Learn File; 14.3 Generate Molecules
THINK Theory Manual: 9.6.1 Visual Inspection
THINK Release Notes: Map Display

donor

THINK User Guide: 4.4 Molecular Properties; 6.2 Set Pharmacophore Options; 10 Docking; 12.4 Select Data to be Analysed
THINK Theory Manual: 3.1.1 Counters; 7.1 Centre Types; 9.5.4 Acid and Base Weighting; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; A.1 Atom Types; Appendix B Pharmacophore File Format

double

THINK User Guide: 1.1 User Interface; 1.5.1 Symbols and Operators; 1.5.2 Script Arguments; 1.5.5 Input and Output; 2.1 Reading Molecules; 3.2 Editing Molecules; 15 Combinatorial Chemistry
THINK Theory Manual: 2 Reading and Saving Files; 2.1.1 Key Features; 2.1.2 Extensions; A.2 Bond Parameters; A.4 Ring Coordinates; A.5 Ring Torsion Angles; 2.5.1 Windows

ELSE, see IF

ELSEIF, see IF

ENDIF, see IF

END

THINK commands: ROTATE
THINK User Guide: 1.5.3 Control Commands and Relational Operators; 1.5.5 Input and Output
THINK Theory Manual: 5 Data Analysis

exact

THINK User Guide: 6.2 Set Pharmacophore Options; 7.1 Molecule and Pharmacophore Inputs; 8 Searching; 8.2 Search Options; 8.4 Perform Search
THINK Theory Manual: 7.2 Fuzzy Pharmacophores; 8 Molecule Searching; 8.1 Substructure Searching; 8.5 Site Searching; 2.5 Starting the Server and Clients; 4.1 Starting the Client; 4.3 Stopping the Client

EXIT

THINK commands: CALCULATE
THINK User Guide: 1.1 User Interface

field

THINK User Guide: 1.4 Identifying Molecules and Atoms; 1.5.6 Intrinsic Functions; 2.1 Reading Molecules; 2.2 Saving Molecules; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.5 View Diversity; 8 Searching; 8.1 Query Molecule Input; 8.2 Search Options; 9.3 Calculate Map; 10.3 Docking Options; 11.6 Define Activity-Based Colour-Coding (2); 12.1 Read Molecules; 12.2 Select Activity Field; 12.3 Set Activity Options; 12.4 Select Data to be Analysed; 12.5 Analyse Data; 13.3 Cluster Molecules; 15.6 Enumeration Options
THINK Theory Manual: 2.1 SMILES; 2.1.2 Extensions; 2.2.1 Key Features; 2.2.2 Extensions; 2.3.2 Extensions; 3.3 User-Defined Properties; 5 Data Analysis; 5.1 Key Features; 6.1 Transformations; 6.2 Application of Earlier Results; 9.6.3 Check Pharmacophores and Conformers; C.2 Constants; 3.1 Graphical Interface (GUI); 3.1.2 Selecting Jobs
THINK Release Notes: De Novo for FBDD; KNIME related changes; Activity Dialog; Activity Profiles; Ligand Query Dialog

FILE

THINK User Guide: 1.1 User Interface; 1.5.1 Symbols and Operators; 1.5.2 Script Arguments; 1.5.5 Input and Output; 2.1 Reading Molecules; 2.2 Saving Molecules; 3.1 Creating Molecules; 4 Visualisation; 4.1 Input Molecules; 5 Conformer Generation; 5.1 Input Molecule(s); 5.5 Generate Conformers; 6 Pharmacophores; 6.1 Input Molecules; 6.4 Calculate Pharmacophores; 8 Searching; 8.1 Query Molecule Input; 8.2 Search Options; 8.4 Perform Search; 8.5 View Search Results; 9 Maps; 10.1 Creating Site Queries; 10.2 Docking Inputs; 10.5 View Docking Results; 11 Property Diversity; 11.1 Identify File to be Processed (1); 11.2 Read Molecules to be Processed (2); 11.7 Calculate Diversity (1,2); 12 Data Analysis; 12.1 Read Molecules; 13 Clustering; 13.1 Input Molecules; 14 De Novo Molecule Generation; 14.1 Input Molecules; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.4 R-group Search; 15.5 Enumeration Inputs; 15.7 Enumeration Results
THINK Theory Manual: 5 Data Analysis; 7.3 Pharmacophore profiles; 9.4 Extended Active Site; 1.2 THINK Jobs
THINK Release Notes: SD files without hydrogens; Profile Comparisons; Saving Pharmacophore Coordinates; Activity Profiles; Side-Chain motion; Script Progress Reports; Map Display; Active Volume Search Constraints; Reading PDB files; Pharmacophore Population Profiles

filter

THINK User Guide: 2.2 Saving Molecules; 3.3 Deleting Molecules; 6.4 Calculate Pharmacophores; 8 Searching; 8.2 Search Options; 10.1 Creating Site Queries; 15 Combinatorial Chemistry; 15.2 R-group Search Options; 15.6 Enumeration Options; 15.7 Enumeration Results
THINK Theory Manual: 5 Data Analysis; 6.2 Application of Earlier Results
THINK Release Notes: De Novo for FBDD

fit

THINK User Guide: 4.2.3 3D Manipulation; 14.2 Set Molecule Creation Options
THINK Theory Manual: 8.5 Site Searching; C.2 Constants; 5 Creating Jobs and Analysing Results
THINK Release Notes: Superimpose; 3D De Novo; Side-Chain motion

functional groups, see keys

GOTO

THINK commands: OPEN
THINK User Guide: 1.5.3 Control Commands and Relational Operators; 1.5.4 Error Handling; 1.5.5 Input and Output

group

THINK commands: DELETE; LEARN
THINK User Guide: 1 Introduction; 1.4 Identifying Molecules and Atoms; 1.5.6 Intrinsic Functions; 3.2 Editing Molecules; 4.2.1 2D Display Mode; 4.2.4 Annotation and Labelling; 4.3 Fingerprint Keys; 4.6 View Atom Data; 8 Searching; 12.4 Select Data to be Analysed; 12.5 Analyse Data; 13 Clustering; 14 De Novo Molecule Generation; 14.2 Set Molecule Creation Options; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.3 R-group Search Output; 15.4 R-group Search; 15.5 Enumeration Inputs; 15.6 Enumeration Options
THINK Theory Manual: 2.1.2 Extensions; 2.2.2 Extensions; 2.3.2 Extensions; 2.3.3 Molecules and Molecule Names; 2.4 Enumeration; 2.4.1 Core-based Libraries; 2.4.2 Coreless Libraries; 2.4.3 Peptide Chains; 3.1.5 Lipophilicity; 5 Data Analysis; 5.3 F-test for Functional Groups; 5.4 F-test for Pharmacophores; 8 Molecule Searching; 8.1 Substructure Searching; 8.2 Similarity Searching; 8.3 R-group Searching; 9.2 Existing Ligand-Protein Complex; 9.3.2 Finding Binding Sites; 9.5 Centre Selection (Weighting); 9.5.1 Required Groups; 9.5.3 Distance Weightings; 9.5.4 Acid and Base Weighting; 9.6.3 Check Pharmacophores and Conformers; A.1 Atom Types; Appendix D ITRACE Values; 3.2 Command Mode
THINK Release Notes: De Novo for FBDD; KNIME; Atom selection; Transformations; Implicit Hydrogens; KNIME related changes; Bug fixes

histogram

THINK User Guide: 4.3 Fingerprint Keys

HELP

THINK commands: LET
THINK User Guide: 1.1 User Interface; 1.5.1 Symbols and Operators

IF

THINK commands: SAVE; SEARCH; SELECT; SUGGEST
THINK User Guide: 1.5 Command Scripts and Symbols; 1.5.3 Control Commands and Relational Operators

insertion code

THINK User Guide: 1.4 Identifying Molecules and Atoms; 4.2.4 Annotation and Labelling

interaction

THINK User Guide: 1.4 Identifying Molecules and Atoms; 4.2 Viewing Molecules; 4.2.4 Annotation and Labelling; 4.4 Molecular Properties; 6 Pharmacophores; 8.5 View Search Results; 9.2 Align Molecules; 10 Docking; 10.1 Creating Site Queries; 10.2 Docking Inputs; 10.3 Docking Options; 10.5 View Docking Results; 14.2 Set Molecule Creation Options
THINK Theory Manual: 8.5 Site Searching; 9.2 Existing Ligand-Protein Complex; 9.6 Reproducing Ligand-Protein Complexes; 9.6.1 Visual Inspection; 9.6.2 Check Site Points; 9.6.3 Check Pharmacophores and Conformers; C.2 Constants; C.3 Flags
THINK Release Notes: De Novo for FBDD; Enumeration for FBDD; Enhancements to Pharmacophore and 3D Searching; Lipophilic centres; Centre Positions; List Distances; KNIME related changes; Side-Chain motion; Molecular Mechanics

Kekule

THINK Theory Manual: 2.1.1 Key Features

keys

THINK commands: DELETE; LEARN
THINK User Guide: 1.5.6 Intrinsic Functions; 3.2 Editing Molecules; 4.2.2 3D Display Mode; 4.2.3 3D Manipulation; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.6 View Atom Data; 8 Searching; 12 Data Analysis; 12.4 Select Data to be Analysed; 12.5 Analyse Data; 13 Clustering; 13.4 View Clusters
THINK Theory Manual: 2.1.1 Key Features; 2.2.1 Key Features; 2.3.1 Key Features; 5 Data Analysis; 5.1 Key Features; 5.4 F-test for Pharmacophores; 8.2 Similarity Searching; 9.1 Complementary Centres; 9.2 Existing Ligand-Protein Complex; 9.6.1 Visual Inspection; C.3 Flags; 1.3.1 Server Queue File; 1.4 THINK Clients
THINK Release Notes: De Novo for FBDD; Atom selection; Minor Graphics Enhancements; Bug fixes

KEY

THINK commands: DELETE
THINK User Guide: 1.5.6 Intrinsic Functions; 4.3 Fingerprint Keys; 12.4 Select Data to be Analysed

LABEL

THINK commands: PLOT
THINK User Guide: 1.5.3 Control Commands and Relational Operators; 1.5.4 Error Handling; 1.5.5 Input and Output

LEARN

THINK commands: ENDIF
THINK User Guide: 12 Data Analysis; 12.2 Select Activity Field; 12.3 Set Activity Options; 12.4 Select Data to be Analysed; 12.5 Analyse Data

LET

THINK commands: READ
THINK User Guide: 1.4 Identifying Molecules and Atoms; 1.5 Command Scripts and Symbols; 1.5.1 Symbols and Operators; 1.5.2 Script Arguments; 1.5.4 Error Handling; 1.5.5 Input and Output
THINK Theory Manual: 3.3 User-Defined Properties; 9.3.1 Site Records in PDB file; 9.6.3 Check Pharmacophores and Conformers; C.3 Flags; 1.2 THINK Jobs
THINK Release Notes: Pharmacophore Profiling Performance

ligand

THINK User Guide: 2.1 Reading Molecules; 4.2 Viewing Molecules; 4.4 Molecular Properties; 8.4 Perform Search; 9 Maps; 9.2 Align Molecules; 9.3 Calculate Map; 9.5 Ligand Query Maps; 10 Docking; 10.1 Creating Site Queries; 10.2 Docking Inputs; 10.3 Docking Options; 15.5 Enumeration Inputs; 15.7 Enumeration Results
THINK Theory Manual: 2.3.3 Molecules and Molecule Names; 8.5 Site Searching; 9 Creating Site Queries; 9.1 Complementary Centres; 9.2 Existing Ligand-Protein Complex; 9.3 List of Active Site Residues; 9.4 Extended Active Site; 9.5.1 Required Groups; 9.5.3 Distance Weightings; 9.5.4 Acid and Base Weighting; 9.6 Reproducing Ligand-Protein Complexes; 9.6.1 Visual Inspection; 9.6.2 Check Site Points; 9.6.3 Check Pharmacophores and Conformers; C.1 Counters; C.2 Constants; C.3 Flags
THINK Release Notes: De Novo for FBDD; 3D De Novo; Water; Centre Positions; List Distances; KNIME related changes; Ligand Query Dialog; Multiple Volume Map Search Constraints; Active Volume Search Constraints; Reading PDB files

lipophile

THINK User Guide: 4 Visualisation; 4.2.2 3D Display Mode; 4.4 Molecular Properties; 4.5 View Diversity; 11 Property Diversity; 11.3 Set Calculation Options (1); 11.5 Select Plot Style (1,2); 11.7 Calculate Diversity (1,2); 12.4 Select Data to be Analysed
THINK Theory Manual: 3.1.5 Lipophilicity; 6.2 Application of Earlier Results; 7.1 Centre Types; A.1 Atom Types; Appendix B Pharmacophore File Format

LIST

THINK commands: CLUSTER
THINK User Guide: 1.5.4 Error Handling; 4 Visualisation; 4.4 Molecular Properties; 4.6 View Atom Data; 5 Conformer Generation; 5.5 Generate Conformers; 6.4 Calculate Pharmacophores; 8 Searching; 12 Data Analysis; 12.6 Apply Learn File
THINK Theory Manual: 9.6.3 Check Pharmacophores and Conformers
THINK Release Notes: List Distances; Scoring functions; List Charges; Map Display; Protein Sites

mapping

THINK User Guide: 4.2.4 Annotation and Labelling; 8.5 View Search Results; 10.5 View Docking Results
THINK Theory Manual: 2.2.2 Extensions; 6 Trouble Shooting

MODIFY

THINK commands: LABEL
THINK User Guide: 1.4 Identifying Molecules and Atoms; 3.2 Editing Molecules; 3.3 Deleting Molecules; 10.1 Creating Site Queries
THINK Theory Manual: 2.3.4 Limitations; 8.3 R-group Searching; 9.2 Existing Ligand-Protein Complex; 9.3.1 Site Records in PDB file; 9.3.2 Finding Binding Sites; 9.4 Extended Active Site
THINK Release Notes: Calculating Bond Orders; Molecular Mechanics

molecule

THINK commands: DISPLAY; KEY
THINK User Guide: 1 Introduction; 1.4 Identifying Molecules and Atoms; 1.5.5 Input and Output; 1.5.6 Intrinsic Functions; 2 Reading and Saving Molecules; 2.1 Reading Molecules; 2.2 Saving Molecules; 3.1 Creating Molecules; 3.2 Editing Molecules; 3.3 Deleting Molecules; 4 Visualisation; 4.1 Input Molecules; 4.2 Viewing Molecules; 4.2.1 2D Display Mode; 4.2.2 3D Display Mode; 4.2.3 3D Manipulation; 4.2.4 Annotation and Labelling; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.5 View Diversity; 4.6 View Atom Data; 5 Conformer Generation; 5.1 Input Molecule(s); 5.2 Set Search Mode; 5.3 Set Bond and Ring Increments; 5.5 Generate Conformers; 6 Pharmacophores; 6.1 Input Molecules; 6.2 Set Pharmacophore Options; 6.4 Calculate Pharmacophores; 7.1 Molecule and Pharmacophore Inputs; 7.3 Subset Calculation; 8 Searching; 8.1 Query Molecule Input; 8.2 Search Options; 8.4 Perform Search; 8.5 View Search Results; 9 Maps; 9.2 Align Molecules; 9.3 Calculate Map; 9.4 Display Map and Molecules; 10 Docking; 10.3 Docking Options; 10.5 View Docking Results; 11.2 Read Molecules to be Processed (2); 11.3 Set Calculation Options (1); 11.7 Calculate Diversity (1,2); 12.6 Apply Learn File; 13 Clustering; 13.3 Cluster Molecules; 13.4 View Clusters; 14 De Novo Molecule Generation; 14.1 Input Molecules; 14.2 Set Molecule Creation Options; 14.3 Generate Molecules; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.4 R-group Search; 15.5 Enumeration Inputs; 15.6 Enumeration Options; 15.7 Enumeration Results
THINK Theory Manual: 1 Introduction; 2 Reading and Saving Files; 2.1 SMILES; 2.1.2 Extensions; 2.2.1 Key Features; 2.3.1 Key Features; 2.3.2 Extensions; 2.3.3 Molecules and Molecule Names; 3.1.2 Volume and Surface Area; 3.1.5 Lipophilicity; 3.3 User-Defined Properties; 4 Conformer Generation; 4.1 Rotational Bonds; 4.2 Conformer Generation; 5 Data Analysis; 5.5 Prediction; 6 De Novo Structure Generation; 6.1 Transformations; 6.2 Application of Earlier Results; 8 Molecule Searching; 8.1 Substructure Searching; 8.2 Similarity Searching; 8.4 3D Searching; 8.5 Site Searching; 8.6 Checkpoint File and Search Tracing; 9.1 Complementary Centres; 9.2 Existing Ligand-Protein Complex; 9.4 Extended Active Site; 9.6 Reproducing Ligand-Protein Complexes; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; Appendix B Pharmacophore File Format; C.1 Counters; C.2 Constants; C.3 Flags; 1.2 THINK Jobs; 1.3 THINK Server; 1.4 THINK Clients; 2.4 Customise "screen.srt"; 4.2.3 Job Information; 5 Creating Jobs and Analysing Results; 6 Trouble Shooting
THINK Release Notes: Cavity Maps; Inter and Intra contact colouring; CUSTOM EXTENT; De Novo for FBDD; Enumeration for FBDD; KNIME Restart; Atom selection; 3D De Novo; Water; SD files without hydrogens; Calculating Bond Orders; Pharmacophore volume and area; KNIME related changes; Bug fixes; Saving Pharmacophore Coordinates; Activity Profiles; Ligand Query Dialog; List Charges; Map Best Plane Projection; Map Display; Active Volume Search Constraints; Molecular Mechanics; Reading PDB files; Pharmacophore Population Profiles

molecule name

THINK User Guide: 1.4 Identifying Molecules and Atoms; 2.1 Reading Molecules; 3.2 Editing Molecules; 4.4 Molecular Properties
THINK Theory Manual: 2.1.2 Extensions; 2.2.1 Key Features; 2.3.1 Key Features; 2.3.2 Extensions; 2.3.3 Molecules and Molecule Names; Appendix B Pharmacophore File Format
THINK Release Notes: KNIME related changes

negative

THINK User Guide: 4.2.2 3D Display Mode; 4.4 Molecular Properties; 10.3 Docking Options
THINK Theory Manual: 3.1.1 Counters; 7.1 Centre Types; 9.1 Complementary Centres; 9.6.1 Visual Inspection; 9.6.2 Check Site Points; A.1 Atom Types; Appendix B Pharmacophore File Format

OPEN

THINK commands: CALL
THINK User Guide: 1.1 User Interface; 1.5.2 Script Arguments; 2.1 Reading Molecules; 3.1 Creating Molecules; 4 Visualisation; 4.1 Input Molecules; 5 Conformer Generation; 5.1 Input Molecule(s); 6 Pharmacophores; 6.1 Input Molecules; 8 Searching; 8.1 Query Molecule Input; 8.5 View Search Results; 9 Maps; 10.5 View Docking Results; 11 Property Diversity; 11.2 Read Molecules to be Processed (2); 12 Data Analysis; 12.1 Read Molecules; 13 Clustering; 13.1 Input Molecules; 14 De Novo Molecule Generation; 14.1 Input Molecules; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.5 Enumeration Inputs
THINK Theory Manual: 5 Data Analysis; 1.2 THINK Jobs
THINK Release Notes: Active Volume Search Constraints; Reading PDB files

open

THINK commands: CALL; WHILE
THINK User Guide: 1 Introduction; 1.1 User Interface; 1.4 Identifying Molecules and Atoms; 1.5.2 Script Arguments; 1.5.5 Input and Output; 2.1 Reading Molecules; 3.1 Creating Molecules; 4 Visualisation; 4.1 Input Molecules; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.5 View Diversity; 5 Conformer Generation; 5.1 Input Molecule(s); 5.5 Generate Conformers; 6 Pharmacophores; 6.1 Input Molecules; 8 Searching; 8.1 Query Molecule Input; 8.4 Perform Search; 8.5 View Search Results; 9 Maps; 9.1 Read Molecules; 10.1 Creating Site Queries; 10.2 Docking Inputs; 10.5 View Docking Results; 11 Property Diversity; 11.1 Identify File to be Processed (1); 11.2 Read Molecules to be Processed (2); 11.7 Calculate Diversity (1,2); 12 Data Analysis; 12.1 Read Molecules; 13 Clustering; 13.1 Input Molecules; 14 De Novo Molecule Generation; 14.1 Input Molecules; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.4 R-group Search; 15.5 Enumeration Inputs
THINK Theory Manual: 1 Introduction; 2 Reading and Saving Files; 2.2 Molfile and SDfile; 2.3.1 Key Features; 2.3.2 Extensions; 2.4 Enumeration; 2.5 Parameter Files; 3.1.5 Lipophilicity; 3.2 3D Calculations; 3.3 User-Defined Properties; 4 Conformer Generation; 5 Data Analysis; 8 Molecule Searching; 8.3 R-group Searching; 8.5 Site Searching; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; Appendix A Parameter File Formats; C.1 Counters; Appendix D ITRACE Values; 1.1 Requirements; 1.2 THINK Jobs; 1.4.1 Files on the Client; 2.2 Configure the Server; 2.4 Customise "screen.srt"; 3.1.3 Buttons and Menus; 5 Creating Jobs and Analysing Results; 6 Trouble Shooting
THINK Release Notes: Profile Comparisons; Map Display; Active Volume Search Constraints; Reading PDB files

read, see open

output

THINK User Guide: 1.3 Log Files; 1.4 Identifying Molecules and Atoms; 1.5.5 Input and Output; 2.1 Reading Molecules; 4 Visualisation; 4.2 Viewing Molecules; 4.2.1 2D Display Mode; 4.2.2 3D Display Mode; 4.2.4 Annotation and Labelling; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.5 View Diversity; 4.6 View Atom Data; 5.5 Generate Conformers; 6 Pharmacophores; 6.4 Calculate Pharmacophores; 7 DiverseSets and FocusedSets; 7.1 Molecule and Pharmacophore Inputs; 7.2 Pharmacophore Options; 8 Searching; 8.1 Query Molecule Input; 8.3 Search Results; 8.4 Perform Search; 8.5 View Search Results; 9.3 Calculate Map; 10 Docking; 10.1 Creating Site Queries; 10.4 Search Results; 10.5 View Docking Results; 11 Property Diversity; 11.4 Supply Results File (1); 11.7 Calculate Diversity (1,2); 12 Data Analysis; 12.6 Apply Learn File; 13 Clustering; 13.2 Set Cluster Options; 13.3 Cluster Molecules; 14 De Novo Molecule Generation; 15 Combinatorial Chemistry; 15.3 R-group Search Output; 15.4 R-group Search
THINK Theory Manual: 4.2 Conformer Generation; 8.6 Checkpoint File and Search Tracing; 9.6.3 Check Pharmacophores and Conformers; C.3 Flags; Appendix D ITRACE Values; 1.2 THINK Jobs; 5 Creating Jobs and Analysing Results; 5.1 Checkpoint Files
THINK Release Notes: Enhancements to Pharmacophore and 3D Searching; KNIME; 3D De Novo; CSV output; KNIME related changes; Ligand Query Dialog; Map Display; Active Volume Search Constraints; Pharmacophore Population Profiles

panel

THINK User Guide: 4 Visualisation; 4.2.2 3D Display Mode; 4.5 View Diversity; 8 Searching; 11.5 Select Plot Style (1,2); 11.7 Calculate Diversity (1,2); 12.6 Apply Learn File; 14.3 Generate Molecules; 2.3 Configure Each Client; 2.3.1 Windows Screen Saver
THINK Release Notes: Additional secondary structure colouring options; Scroll Bar; Bug fixes; Minor Graphics Enhancements

parameter

THINK commands: WHILE; WRITE
THINK Theory Manual: 2 Reading and Saving Files; 2.5 Parameter Files; A.2 Bond Parameters; A.4 Ring Coordinates; A.5 Ring Torsion Angles
THINK Release Notes: Protein Sites

PFA

THINK User Guide: 4.4 Molecular Properties; 12.4 Select Data to be Analysed
THINK Theory Manual: 3.1.3 Partial Surface Areas

pharmacophore

THINK commands: HELP
THINK User Guide: 1 Introduction; 4.2 Viewing Molecules; 6 Pharmacophores; 6.1 Input Molecules; 6.2 Set Pharmacophore Options; 6.3 Set Conformer Options; 6.4 Calculate Pharmacophores; 7 DiverseSets and FocusedSets; 7.1 Molecule and Pharmacophore Inputs; 7.2 Pharmacophore Options; 8 Searching; 8.1 Query Molecule Input; 8.2 Search Options; 8.4 Perform Search; 8.5 View Search Results; 9 Maps; 9.2 Align Molecules; 9.5 Ligand Query Maps; 10 Docking; 10.3 Docking Options
THINK Theory Manual: 5 Data Analysis; 5.4 F-test for Pharmacophores; 7.2 Fuzzy Pharmacophores; 7.3 Pharmacophore profiles; 7.4 Pharmacophore Files; 8 Molecule Searching; 8.4 3D Searching; 8.5 Site Searching; 9.5.1 Required Groups; 9.5.2 Pharmacophore Score; 9.5.3 Distance Weightings; 9.5.4 Acid and Base Weighting; 9.6.3 Check Pharmacophores and Conformers; Appendix B Pharmacophore File Format; C.1 Counters; C.2 Constants; C.3 Flags; Appendix D ITRACE Values
THINK Release Notes: CUSTOM EXTENT; THINK v2.00a; De Novo for FBDD; Enhancements to Pharmacophore and 3D Searching; KNIME; 3D De Novo; KNIME; Pharmacophore volume and area; THINK v1.32g; Pharmacophore Profiles; Saving Pharmacophore Coordinates; Pharmacophore Profiling Performance; Ligand Query Dialog; Multiple Volume Map Search Constraints; Conformational Generation; Bug fixes; Active Volume Search Constraints; THINK v1.30; Molecular Mechanics; Pharmacophore Population Profiles

PLOT

THINK commands: KEY
THINK User Guide: 4.2 Viewing Molecules; 4.2.2 3D Display Mode; 4.3 Fingerprint Keys; 4.5 View Diversity

polar surface area

THINK User Guide: 4.4 Molecular Properties; 12.4 Select Data to be Analysed
THINK Theory Manual: 3.1.3 Partial Surface Areas

positive

THINK User Guide: 4.2.2 3D Display Mode; 4.4 Molecular Properties
THINK Theory Manual: 3.1.1 Counters; 7.1 Centre Types; 9.1 Complementary Centres; 9.6.1 Visual Inspection; A.1 Atom Types; Appendix B Pharmacophore File Format

PSA, see polar surface area

R-group

THINK User Guide: 3.2 Editing Molecules; 4.2.1 2D Display Mode; 8 Searching; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.3 R-group Search Output; 15.4 R-group Search; 15.5 Enumeration Inputs; 15.6 Enumeration Options; 15.7 Enumeration Results
THINK Theory Manual: 2.1.2 Extensions; 2.2.2 Extensions; 2.4 Enumeration; 2.4.1 Core-based Libraries; 2.4.2 Coreless Libraries; 2.4.3 Peptide Chains; 8 Molecule Searching; 8.3 R-group Searching; Appendix D ITRACE Values
THINK Release Notes: Enumeration for FBDD; KNIME; 2D Edit; Implicit Hydrogens

radius

THINK User Guide: 4.2 Viewing Molecules; 4.2.4 Annotation and Labelling; 4.4 Molecular Properties; 5.4 Set Contacts Check; 6.3 Set Conformer Options; 8.2 Search Options; 12.4 Select Data to be Analysed
THINK Theory Manual: 2.5 Parameter Files; 3.1.2 Volume and Surface Area; 3.1.5 Lipophilicity; 3.2.1 CPK Contacts; 3.2.2 VdW Contacts; 4.2 Conformer Generation; 4.3 Contacts Check; 8.4 3D Searching; 8.5 Site Searching; 9.1 Complementary Centres; 9.2 Existing Ligand-Protein Complex; 9.4 Extended Active Site; 9.5.3 Distance Weightings; 9.6.1 Visual Inspection; 9.6.3 Check Pharmacophores and Conformers; A.1 Atom Types; C.2 Constants; C.3 Flags
THINK Release Notes: De Novo for FBDD; Enumeration for FBDD; Side-Chain motion; Map Display

ratio, see radius

READ

THINK commands: WHILE
THINK User Guide: 1.5.5 Input and Output
THINK Release Notes: Profile Comparisons

reject

THINK User Guide: 10.3 Docking Options
THINK Release Notes: Reject and Learn default file names

residue

THINK User Guide: 1.4 Identifying Molecules and Atoms; 4.2.2 3D Display Mode; 4.2.4 Annotation and Labelling; 10 Docking; 10.1 Creating Site Queries; 10.3 Docking Options; 14.2 Set Molecule Creation Options; 15.6 Enumeration Options
THINK Theory Manual: 2.3 PDB Format; 2.3.1 Key Features; 2.3.4 Limitations; 8.5 Site Searching; 9.3 List of Active Site Residues; 9.3.2 Finding Binding Sites
THINK Release Notes: De Novo for FBDD; Residue Connectivity; Reading PDB files; Protein Sites; Minor Graphics Enhancements

RETURN

THINK commands: MODIFY
THINK User Guide: 1.5 Command Scripts and Symbols; 1.2 THINK Jobs

ring

THINK User Guide: 1 Introduction; 3.2 Editing Molecules; 4.2.2 3D Display Mode; 4.4 Molecular Properties; 5.2 Set Search Mode; 5.3 Set Bond and Ring Increments; 6.3 Set Conformer Options; 10 Docking; 12.4 Select Data to be Analysed
THINK Theory Manual: 2 Reading and Saving Files; 2.1.1 Key Features; 2.1.2 Extensions; 2.5 Parameter Files; 3.1.1 Counters; 3.1.5 Lipophilicity; 4.1 Rotational Bonds; 5.4 F-test for Pharmacophores; 7.1 Centre Types; 8.1 Substructure Searching; 8.4 3D Searching; 9.1 Complementary Centres; A.1 Atom Types; A.4 Ring Coordinates; A.5 Ring Torsion Angles; Appendix B Pharmacophore File Format; C.2 Constants; C.3 Flags
THINK Release Notes: 3D Coordinate Generator; Bridged rings; Centre Positions; Calculating Bond Orders; Molecular Mechanics

ROTATE

THINK commands: IF
THINK User Guide: 1.4 Identifying Molecules and Atoms; 4.2.3 3D Manipulation
THINK Release Notes: Map Best Plane Projection

SAVE

THINK commands: CHECK
THINK User Guide: 1.1 User Interface; 2.2 Saving Molecules; 5.5 Generate Conformers; 6 Pharmacophores; 6.4 Calculate Pharmacophores; 10.1 Creating Site Queries; 15 Combinatorial Chemistry; 15.5 Enumeration Inputs; 15.6 Enumeration Options; 15.7 Enumeration Results
THINK Theory Manual: 5 Data Analysis; 7.3 Pharmacophore profiles; 9.4 Extended Active Site
THINK Release Notes: SD files without hydrogens; Saving Pharmacophore Coordinates; Activity Profiles; Map Display; Active Volume Search Constraints; Pharmacophore Population Profiles

save

THINK commands: CHECK; WRITE
THINK User Guide: 1.1 User Interface; 1.2 Error Messages; 1.5.4 Error Handling; 1.5.5 Input and Output; 2.2 Saving Molecules; 3.2 Editing Molecules; 4.2 Viewing Molecules; 4.2.1 2D Display Mode; 4.4 Molecular Properties; 5.5 Generate Conformers; 6 Pharmacophores; 6.4 Calculate Pharmacophores; 9.4 Display Map and Molecules; 10.1 Creating Site Queries; 11 Property Diversity; 15 Combinatorial Chemistry; 15.5 Enumeration Inputs; 15.6 Enumeration Options; 15.7 Enumeration Results
THINK Theory Manual: 2 Reading and Saving Files; 2.2 Molfile and SDfile; 2.2.2 Extensions; 2.4 Enumeration; 2.5 Parameter Files; 3.3 User-Defined Properties; 5 Data Analysis; 7.3 Pharmacophore profiles; 9.4 Extended Active Site; C.3 Flags; 1.1 Requirements; 1.3 THINK Server; 1.3.1 Server Queue File; 1.4.1 Files on the Client; 2.2 Configure the Server; 2.3 Configure Each Client; 5 Creating Jobs and Analysing Results; 6 Trouble Shooting
THINK Release Notes: KNIME; KNIME; 2D Edit; KNIME; KNIME; SD files without hydrogens; KNIME related changes; Saving Pharmacophore Coordinates; Activity Profiles; Map Display; Active Volume Search Constraints; Pharmacophore Population Profiles

score

THINK User Guide: 4.4 Molecular Properties; 10 Docking; 10.3 Docking Options; 14.2 Set Molecule Creation Options; 15.6 Enumeration Options
THINK Theory Manual: 8.5 Site Searching; 9.5.2 Pharmacophore Score; 9.5.3 Distance Weightings; 9.5.4 Acid and Base Weighting; 9.6.3 Check Pharmacophores and Conformers; C.2 Constants; Appendix D ITRACE Values
THINK Release Notes: De Novo for FBDD; KNIME related changes; Scoring functions

SD

THINK User Guide: 1.1 User Interface; 1.4 Identifying Molecules and Atoms; 2 Reading and Saving Molecules; 2.1 Reading Molecules; 2.2 Saving Molecules; 4.1 Input Molecules; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.5 View Diversity; 5.1 Input Molecule(s); 5.5 Generate Conformers; 6.1 Input Molecules; 6.4 Calculate Pharmacophores; 7 DiverseSets and FocusedSets; 7.1 Molecule and Pharmacophore Inputs; 8.1 Query Molecule Input; 8.2 Search Options; 8.3 Search Results; 8.4 Perform Search; 8.5 View Search Results; 9.1 Read Molecules; 10.2 Docking Inputs; 10.4 Search Results; 10.5 View Docking Results; 11.1 Identify File to be Processed (1); 11.4 Supply Results File (1); 12.1 Read Molecules; 13.1 Input Molecules; 13.3 Cluster Molecules; 14 De Novo Molecule Generation; 14.1 Input Molecules; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.3 R-group Search Output
THINK Theory Manual: 2 Reading and Saving Files; 2.3.1 Key Features; 3.2 3D Calculations; 3.3 User-Defined Properties; 8 Molecule Searching; 8.4 3D Searching; 8.5 Site Searching; 9.6.3 Check Pharmacophores and Conformers
THINK Release Notes: Text Fields; Implicit Hydrogens; SD files without hydrogens; KNIME related changes; Pharmacophore Population Profiles

SDF, see SD

SEARCH

THINK commands: CUSTOMISE
THINK User Guide: 8 Searching; 8.2 Search Options; 8.3 Search Results; 8.4 Perform Search; 10.2 Docking Inputs; 10.3 Docking Options; 15 Combinatorial Chemistry; 15.2 R-group Search Options; 15.3 R-group Search Output; 15.4 R-group Search
THINK Theory Manual: 9.6.3 Check Pharmacophores and Conformers; 1.2 THINK Jobs; 5 Creating Jobs and Analysing Results
THINK Release Notes: Side-Chain motion; Active Volume Search Constraints

SELECT

THINK commands: HELP
THINK User Guide: 11 Property Diversity; 11.1 Identify File to be Processed (1); 11.3 Set Calculation Options (1); 11.4 Supply Results File (1); 11.5 Select Plot Style (1,2); 11.7 Calculate Diversity (1,2)
THINK Release Notes: List Distances; Map Display; Protein Sites; Pharmacophore Population Profiles

sequence

THINK User Guide: 1.4 Identifying Molecules and Atoms; 4.2.4 Annotation and Labelling; 10.2 Docking Inputs
THINK Theory Manual: 2.3.1 Key Features; 9.3 List of Active Site Residues; 9.3.1 Site Records in PDB file
THINK Release Notes: Ligand Query Dialog; Protein Sites

serial

THINK User Guide: 1.4 Identifying Molecules and Atoms; 2 Reading and Saving Molecules; 3.2 Editing Molecules; 4.2.4 Annotation and Labelling; 4.4 Molecular Properties; 10.4 Search Results
THINK Theory Manual: 2.2.2 Extensions; 8.4 3D Searching; 8.5 Site Searching; 9.5.1 Required Groups; 9.6.3 Check Pharmacophores and Conformers

shape, see conformer

significance

THINK User Guide: 4.3 Fingerprint Keys; 12 Data Analysis; 12.3 Set Activity Options; 12.5 Analyse Data; 14.3 Generate Molecules
THINK Theory Manual: 5.1 Key Features; C.2 Constants
THINK Release Notes: Activity Dialog; Activity Profiles

similarity

THINK User Guide: 1 Introduction; 4.1 Input Molecules; 4.2 Viewing Molecules; 4.2.1 2D Display Mode; 8 Searching; 8.2 Search Options; 8.3 Search Results; 8.4 Perform Search; 13 Clustering; 13.2 Set Cluster Options; 13.3 Cluster Molecules
THINK Theory Manual: 6 De Novo Structure Generation; 6.2 Application of Earlier Results; 8 Molecule Searching; 8.2 Similarity Searching
THINK Release Notes: KNIME

site

THINK User Guide: 1 Introduction; 1.4 Identifying Molecules and Atoms; 1.5.6 Intrinsic Functions; 4.2.2 3D Display Mode; 4.2.3 3D Manipulation; 4.2.4 Annotation and Labelling; 4.4 Molecular Properties; 6 Pharmacophores; 8 Searching; 8.3 Search Results; 8.4 Perform Search; 9 Maps; 9.1 Read Molecules; 9.4 Display Map and Molecules; 9.5 Ligand Query Maps; 10 Docking; 10.1 Creating Site Queries; 10.2 Docking Inputs; 10.3 Docking Options; 10.4 Search Results; 10.5 View Docking Results; 15 Combinatorial Chemistry; 15.2 R-group Search Options; 15.4 R-group Search; 15.6 Enumeration Options
THINK Theory Manual: 1 Introduction; 2.3.1 Key Features; 2.3.2 Extensions; 2.3.3 Molecules and Molecule Names; 4.1 Rotational Bonds; 4.2 Conformer Generation; 6.1 Transformations; 8 Molecule Searching; 8.5 Site Searching; 9 Creating Site Queries; 9.1 Complementary Centres; 9.2 Existing Ligand-Protein Complex; 9.3 List of Active Site Residues; 9.3.1 Site Records in PDB file; 9.3.2 Finding Binding Sites; 9.4 Extended Active Site; 9.5 Centre Selection (Weighting); 9.5.1 Required Groups; 9.5.3 Distance Weightings; 9.5.4 Acid and Base Weighting; 9.6 Reproducing Ligand-Protein Complexes; 9.6.1 Visual Inspection; 9.6.2 Check Site Points; 9.6.3 Check Pharmacophores and Conformers; C.1 Counters; C.2 Constants; C.3 Flags; 1.1 Requirements; 1.2 THINK Jobs; 4.2.3 Job Information; 5 Creating Jobs and Analysing Results
THINK Release Notes: Cavity Maps; De Novo for FBDD; 3D De Novo; Water; Centre Positions; Pharmacophore volume and area; Bug fixes; Side-Chain motion; Multiple Volume Map Search Constraints; Active Volume Search Constraints; Reading PDB files; Protein Sites; Minor Graphics Enhancements

site-points, see centres

SMILES

THINK User Guide: 1.1 User Interface; 1.4 Identifying Molecules and Atoms; 1.5.6 Intrinsic Functions; 2 Reading and Saving Molecules; 2.1 Reading Molecules; 2.2 Saving Molecules; 3.1 Creating Molecules; 4.1 Input Molecules; 4.3 Fingerprint Keys; 4.4 Molecular Properties; 4.5 View Diversity; 5.1 Input Molecule(s); 5.5 Generate Conformers; 6.1 Input Molecules; 7 DiverseSets and FocusedSets; 7.1 Molecule and Pharmacophore Inputs; 8.1 Query Molecule Input; 8.2 Search Options; 8.3 Search Results; 8.5 View Search Results; 10.2 Docking Inputs; 10.4 Search Results; 10.5 View Docking Results; 11.1 Identify File to be Processed (1); 11.4 Supply Results File (1); 12.1 Read Molecules; 13.1 Input Molecules; 13.3 Cluster Molecules; 14 De Novo Molecule Generation; 14.1 Input Molecules; 14.2 Set Molecule Creation Options; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.3 R-group Search Output; 15.7 Enumeration Results
THINK Theory Manual: 2 Reading and Saving Files; 2.1 SMILES; 2.1.1 Key Features; 2.1.2 Extensions; 2.2.2 Extensions; 2.3.1 Key Features; 2.4 Enumeration; 3.3 User-Defined Properties; 6.1 Transformations; 6.3 Rejections File; 8 Molecule Searching; 8.2 Similarity Searching; 8.3 R-group Searching; 8.4 3D Searching; 5 Creating Jobs and Analysing Results
THINK Release Notes: Text Fields; KNIME related changes

substructure

THINK User Guide: 1 Introduction; 1.5.6 Intrinsic Functions; 2.1 Reading Molecules; 2.2 Saving Molecules; 8 Searching; 8.1 Query Molecule Input; 8.2 Search Options; 8.4 Perform Search; 14 De Novo Molecule Generation; 15.1 R-group Search Input; 15.5 Enumeration Inputs
THINK Theory Manual: 6 De Novo Structure Generation; 6.3 Rejections File; 8 Molecule Searching; 8.1 Substructure Searching; 8.3 R-group Searching; 8.4 3D Searching; 8.5 Site Searching; C.2 Constants; Appendix D ITRACE Values

superimpose, see fit

surface area

THINK User Guide: 4.4 Molecular Properties
THINK Theory Manual: 3.1.2 Volume and Surface Area; 3.1.3 Partial Surface Areas

SUGGEST

THINK commands: ELSEIF
THINK User Guide: 1.1 User Interface; 12.6 Apply Learn File; 14 De Novo Molecule Generation; 14.2 Set Molecule Creation Options; 14.3 Generate Molecules
THINK Release Notes: 3D De Novo

time

THINK User Guide: 1.3 Log Files; 1.4 Identifying Molecules and Atoms; 1.5.6 Intrinsic Functions; 5.2 Set Search Mode; 8.2 Search Options; 8.4 Perform Search; 10.3 Docking Options; 15.2 R-group Search Options; 15.4 R-group Search
THINK Theory Manual: 3.1.5 Lipophilicity; 4.2 Conformer Generation; 4.3 Contacts Check; 8.6 Checkpoint File and Search Tracing; 9.2 Existing Ligand-Protein Complex; 9.6.3 Check Pharmacophores and Conformers; C.2 Constants; Appendix D ITRACE Values; 1 Introduction; 1.4 THINK Clients; 3.1 Graphical Interface (GUI); 3.1.3 Buttons and Menus; 3.2 Command Mode; 3.2.2 General Options; 4.2.3 Job Information; 6 Trouble Shooting
THINK Release Notes: KNIME Node Speed; KNIME Restart; Atom selection; 3D De Novo; Multiple Volume Map Search Constraints; Conformational Generation; Multiple copies

timeout, see time

tolerance

THINK User Guide: 6.2 Set Pharmacophore Options; 7.1 Molecule and Pharmacophore Inputs; 7.2 Pharmacophore Options; 8.2 Search Options; 10.1 Creating Site Queries; 10.3 Docking Options
THINK Theory Manual: 2.3.2 Extensions; 7.2 Fuzzy Pharmacophores; 8.4 3D Searching; 8.5 Site Searching; 9.1 Complementary Centres; Appendix B Pharmacophore File Format; C.2 Constants; C.3 Flags
THINK Release Notes: Centre Positions; Ligand Query Dialog; Active Volume Search Constraints

transforms

THINK User Guide: 14.2 Set Molecule Creation Options; 14.3 Generate Molecules
THINK Release Notes: Transformations

type

THINK commands: WRITE
THINK User Guide: 1.4 Identifying Molecules and Atoms; 2 Reading and Saving Molecules; 3.2 Editing Molecules; 4.2 Viewing Molecules; 4.2.2 3D Display Mode; 4.2.3 3D Manipulation; 4.2.4 Annotation and Labelling; 5.3 Set Bond and Ring Increments; 6.1 Input Molecules; 6.3 Set Conformer Options; 8 Searching; 8.2 Search Options; 8.3 Search Results; 9 Maps; 9.3 Calculate Map; 15 Combinatorial Chemistry; 15.1 R-group Search Input; 15.2 R-group Search Options; 15.7 Enumeration Results
THINK Theory Manual: 2.1.2 Extensions; 2.2.2 Extensions; 2.4 Enumeration; 2.4.1 Core-based Libraries; 7.1 Centre Types; 8.1 Substructure Searching; 8.3 R-group Searching; 9.1 Complementary Centres; Appendix A Parameter File Formats; A.1 Atom Types; A.2 Bond Parameters; A.3 Angle Parameters; A.4 Ring Coordinates; A.5 Ring Torsion Angles; Appendix B Pharmacophore File Format; Appendix D ITRACE Values; 2 Installing THINK for Use in Client-Serv; 6 Trouble Shooting
THINK Release Notes: Cavity Maps; Additional secondary structure colouring options; Transformations; Activity Dialog; Saving Pharmacophore Coordinates; Ligand Query Dialog; Map Display; Active Volume Search Constraints; Molecular Mechanics

VdW, see radius

volume

THINK User Guide: 1 Introduction; 1.1 User Interface; 4.2 Viewing Molecules; 4.4 Molecular Properties; 4.5 View Diversity; 6 Pharmacophores; 6.4 Calculate Pharmacophores; 8 Searching; 8.5 View Search Results; 9 Maps; 9.3 Calculate Map; 9.4 Display Map and Molecules; 9.5 Ligand Query Maps; 10.3 Docking Options; 11 Property Diversity; 11.3 Set Calculation Options (1); 11.5 Select Plot Style (1,2); 11.7 Calculate Diversity (1,2); 12.4 Select Data to be Analysed; 14.2 Set Molecule Creation Options; 15.6 Enumeration Options
THINK Theory Manual: 3.1.2 Volume and Surface Area; 8.5 Site Searching; 9.6.3 Check Pharmacophores and Conformers; C.2 Constants
THINK Release Notes: CUSTOM EXTENT; 3D De Novo; Pharmacophore volume and area; Pharmacophore Profiling Performance; Ligand Query Dialog; Multiple Volume Map Search Constraints; THINK v1.31; Map Display; Active Volume Search Constraints

WHILE

THINK commands: RETURN
THINK User Guide: 1.5 Command Scripts and Symbols; 1.5.3 Control Commands and Relational Operators
THINK Theory Manual: 5 Data Analysis

wildcard

THINK User Guide: 2.1 Reading Molecules; 3.2 Editing Molecules; 15.1 R-group Search Input
THINK Theory Manual: 8.3 R-group Searching; A.1 Atom Types

write molecules, see SAVE

WRITE

THINK commands: WRITE
THINK User Guide: 1.5.4 Error Handling; 1.5.5 Input and Output
THINK Theory Manual: 5 Data Analysis

XFA

THINK User Guide: 4.4 Molecular Properties; 12.4 Select Data to be Analysed
THINK Theory Manual: 3.1.3 Partial Surface Areas

XSA

THINK User Guide: 4.4 Molecular Properties; 12.4 Select Data to be Analysed
THINK Theory Manual: 3.1.3 Partial Surface Areas