- 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