• 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

New program feature request

The QIAGEN Aarhus team is continuously improving the CLC Drug Discovery Workbench with our users' interests in mind. We welcome all requests and feedback from users, as well as suggestions for new features or more general improvements to the program. To contact us via the Workbench, please go to the menu option:

        Help | Contact Support

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