Manuals
Browse the manual
Introduction to CLC Drug Discovery Workbench
Contact information
Contact for the CLC Drug Discovery Workbench
New program feature request
Getting help
Download and installation
Program download
Installation on Microsoft Windows
Installation on Mac OS X
Installation on Linux with an installer
System requirements
Limitations on maximum number of cores
Workbench Licenses
Request an evaluation license
Download a license using a license order ID
Import a license from a file
Upgrade license
Configure license server connection
Download a static license on a non-networked machine
Limited mode
Start in safe mode
When the program is installed: Getting started
Quick start
Import of example data
Plugins
Installing plugins
Uninstalling plugins
Updating plugins
Network configuration
User interface
View Area
Open view
Open additional views with the toolbar
History and Info views
Close views
Save changes in a view
Undo/Redo
Arrange views in View Area
Moving a view to a different screen
Side Panel
Zoom and selection in View Area
Zoom in
Zoom out
Selecting, panning and zooming
Toolbox and Status Bar
Processes
Toolbox
Status Bar
Workspace
Create Workspace
Select Workspace
Delete Workspace
Data management and search
Navigation Area
Data structure
Create new folders
Sorting folders
Multiselecting elements
Moving and copying elements
Change element names
Delete, restore and remove elements
Show folder elements in a table
Metadata
Importing Metadata
Associating data elements with metadata
Working with data and metadata
Working with tables
Filtering tables
Customized attributes on data locations
Configuring which fields should be available
Editing lists
Removing attributes
Changing the order of the attributes
Filling in values
What happens when a clc object is copied to another data location?
Searching
Local search
What kind of information can be searched?
Quick search
Advanced search
Search index
User preferences and settings
General preferences
View preferences
Import and export Side Panel settings
Advanced preferences
Export/import of preferences
The different options for export and import
View settings for the Side Panel
Saving, removing and applying saved settings
Printing
Selecting which part of the view to print
Page setup
Print preview
Import/export of data and graphics
Standard import
Import using the import dialog
Import using drag and drop
Import using copy/paste of text
External files
Import molecules
Using the standard importer
Using Import Molecules with 3D Coordinates
Add Molecules to Molecule Project
From the Protein Data Bank
BLAST search against the PDB database
Import Molecules from SMILES or 2D
Copy-paste of SMILES strings
Generation of 3D structure on import
Import issues
Data export
Export of folders and multiple elements in CLC format
Export of dependent elements
The CLC format
Backing up data from the CLC Workbench
Export of tables
Export graphics to files
Which part of the view to export
Save location and file formats
Graphics export parameters
Exporting protein reports
Export graph data points to a file
Copy/paste view output
Data download
Search for structures at NCBI
Structure search options
Handling of NCBI structure search results
Save structure search parameters
UniProt (Swiss-Prot/TrEMBL) search
UniProt search options
Handling of UniProt search results
Save UniProt search parameters
Sequence web info
Running tools, handling results and batching
Running tools
Handling results
Batch processing
Standard batch processing
Batch overview
Parameters for batch runs
Running the analysis and organizing the results
Batch launching workflows with multiple inputs
Workflows
Creating a workflow
Adding workflow elements
Configuring workflow elements
Locking and unlocking parameters
Connecting workflow elements
Output
Input
Layout
Input modifying tools
Workflow validation
Workflow creation helper tools
Adding to workflows
Snippets in workflows
Change the order of tracks in the Genome Browser View
Distributing and installing workflows
Creating a workflow installation file
Installing a workflow
Managing workflows
Workflow identification and versioning
Automatic update of workflow elements
Executing a workflow
Open copy of installed workflow
Drug design
Viewing molecular structures in 3D
Moving and rotating
Troubleshooting 3D graphics errors
Customizing the visualization
Visualization styles and colors
Project settings
Snapshots of the molecule visualization
Tools for linking sequence and structure
Show sequence associated with molecule
Link sequence or sequence alignment to structure
Transfer annotations between sequence and structure
Protein structure alignment
The Align Protein Structure dialog box
Example: alignment of calmodulin
The Align Protein Structure algorithm
Generate Biomolecule
Molecule Tables
Create Molecule Table
Grid view of molecule 2D depictions
Viewing Molecule Table structures in 3D
Docking Results Tables
Editing molecule objects
Editing atom and bond properties
Converting molecules to Cofactors or Ligands
The Protein Optimizer
The selection panel
The issues panel
The modify residue panel
The modify surrounding residues panel
The visualization panel
How side chains are modeled
The Ligand Optimizer
The 2D depiction panel
The issues panel
The modify panel
The properties & interactions panel
The constraints panel
Molecular docking
Setup Binding Site
Ligand docking using the Dock Ligands tool
Ligand docking from the Project Tree
The docking algorithms
Inspecting docking results
Screen ligands
Improving docking and screening accuracy
Docking
Screening
Protein Target
Ligand
Screening library
Docking simulation
Screening simulation
Find potential binding pockets
The Find Binding Pockets algorithm
Calculate molecular properties
The log P algorithm
Extract ligands
Viewing and editing sequences
View sequence
Sequence settings in Side Panel
Selecting parts of the sequence
Editing the sequence
Sequence region types
Circular DNA
Using split views to see details of the circular molecule
Mark molecule as circular and specify starting point
Working with annotations
Viewing annotations
Adding annotations
Edit annotations
Removing annotations
Element information
View as text
Sequence Lists
BLAST search
Running BLAST searches
BLAST at NCBI
BLAST a partial sequence against NCBI
BLAST against local data
BLAST a partial sequence against a local database
Output from BLAST searches
Graphical overview for each query sequence
Overview BLAST table
BLAST graphics
BLAST HSP table
BLAST hit table
Extract consensus sequence
Local BLAST databases
Make pre-formatted BLAST databases available
Download NCBI pre-formatted BLAST databases
Create local BLAST databases
Manage BLAST databases
Bioinformatics explained: BLAST
Examples of BLAST usage
Searching for homology
How does BLAST work?
Which BLAST program should I use?
Which BLAST options should I change?
Explanation of the BLAST output
I want to BLAST against my own sequence database, is this possible?
What you cannot get out of BLAST
Other useful resources
Sequence analyses
Find and Model Structure
Create structure model
Method details
Download Find Structure Database
Extract sequences
Dot plots
Create dot plots
View dot plots
Bioinformatics explained: Dot plots
Realization of dot plots
Examples and interpretations of dot plots
Bioinformatics explained: Scoring matrices
Different scoring matrices
Use of scoring matrices
Sequence statistics
Bioinformatics explained: Protein statistics
Pattern discovery
Pattern discovery search parameters
Pattern search output
Motif Search
Dynamic motifs
Motif search from the Toolbox
Java regular expressions
Create motif list
Signal peptide prediction
Bioinformatics explained: Prediction of signal peptides
Why the interest in signal peptides?
Different types of signal peptides
Prediction of signal peptides and subcellular localization
The SignalP method
What do the SignalP scores mean?
Transmembrane helix prediction
Hydrophobicity
Hydrophobicity plot
Hydrophobicity graphs along sequence
Bioinformatics explained: Protein hydrophobicity
Hydrophobicity scales
Pfam domain search
Download of Pfam database
Running Pfam Domain Search
Secondary structure prediction
Sequence alignment
Create an alignment
Gap costs
Fast or accurate alignment algorithm
Aligning alignments
Fixpoints
View alignments
Bioinformatics explained: Sequence logo
Calculation of sequence logos
Edit alignments
Move residues and gaps
Insert gaps
Delete residues and gaps
Copy annotations to other sequences
Move sequences up and down
Delete and rename sequences
Delete, rename and add sequences
Realignment
Pairwise comparison
Pairwise comparison on alignment selection
Pairwise comparison parameters
The pairwise comparison table
Bioinformatics explained: Multiple alignments
Use of multiple alignments
Constructing multiple alignments
Phylogenetic tree features
Create Trees
Create tree
Bioinformatics explained
Tree Settings
Minimap
Tree layout
Node settings
Label settings
Background settings
Branch layout
Bootstrap settings
Visualizing metadata
Node right click menu
Metadata and phylogenetic trees
Table Settings and Filtering
Add or modify metadata on a tree
Undefined metadata values on a tree
Selection of specific nodes
Appendix
Use of multi-core computers
Graph preferences
BLAST databases
Peptide sequence databases
Nucleotide sequence databases
Adding more databases
IUPAC codes for amino acids
IUPAC codes for nucleotides
Formats for import and export
List of bioinformatic data formats
List of graphics data formats
Matrices for alignment calculation
PAM30 log-odds matrix
PAM60 log-odds matrix
BLOSUM42 log-odds matrix
BLOSUM62 log-odds matrix
BLOSUM80 log-odds matrix
Bibliography
Visualization styles and colors
Subsections
Wireframe, Stick, Ball and stick, Space-filling/CPK
Backbone
Surfaces
Labels
Hydrogen bonds
Create atom group
Zoom to fit