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CADDSuite - A flexible and open workflow-enabled framework for computer-aided drug design

CADDSuite offers modular tools for most commonly used tasks in the field of computer-aided drug design, that all have the same interface and can easily be used to create even complex workflows.

There are algorithms and tools for data storage and retrieval, data preparation, chemical checks, QSAR, Docking, Rescoring and for the analysis of results.

CADDSuite has also been integrated into the workflow system Galaxy, in order to make submitting jobs (to a cluster/cloud/grid) or creating, modifying or starting workflows even easier for the user. In essence, a user can thus easily create drug-design pipelines directly from a web browser, without any need for software installations on his local computer.

See the bottom of this page for a list and short description of all contained tools. Furthermore, have a look at the tutorial for some examples showing how to use these tools.

 

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Contact

 For feedback, suggestions or questions contact Oliver Kohlbacher (Oliver.Kohlbacher (AT) uni-tuebingen.de)

Downloads

     CADDSuite 1.5 is currently available from the Git repository of BALL and will soon be released as a binary package and as part of KNIME.

     

    License

     CADDSuite is available free of charge, licensed under the GNU GPL.

     

    Contained tools

     There are tools for the following tasks: 

    Get Data:

    • CombiLibGenerator: generate R-group decorated ligands

    • DBExporter: fetch (filtered) molecules from DB

    Preparation of input data:

    • PDBCutter: separate ligand and receptor

    • ProteinProtonator: protonate protein structures

    • BindingDBCleaner: fix data from bindingdb.org

    • EvenSplit: generate splits w/ equal property range

    • PropertyModifier: modify property tags

    • LigandFileSplitter: split molecule files

    • Ligand3DGenerator: generate 3D coordinates for small molecules

    Structure checks and evaluations:

    • ProteinCheck: evaluate protein quality

    • LigCheck: chemical sanity check for ligands

    QuEasy (QSAR):

    • InputReader: read molecules and generate features

    • ModelCreator: create a QSAR model

    • FeatureSelector: automatically select features of a QSAR model

    • Validator: evaluate quality of a QSAR model

    • MolPredictor: predict molecule activities with QSAR model

    • AutoModel: automatically find best QSAR model

    Docking:

    • WaterFinder: find strongly bound water molecules

    • SpatialConstraintDefiner: define spatial constraint

    • InteractionConstraintDefiner: define interaction constraint

    • ConstraintsFinder: find strongly interacting residues

    • PocketDetector: detect ligand binding pocket

    • GridBuilder: precalculate grids for docking

    • IMGDock: run Iterative Multi-Greedy Docking

    Rescoring:

    • SimpleRescorer: rescore docking results

    • TaGRes-train: Target-specific Grid-Rescoring, training

    • TaGRes: Target-specific Grid-Rescoring

    • AntitargetRescoring: rescore w/ respect to antitarget

    Analysis:

    • ScoreAnalyzer: generate ROC or enrichment plots

    • SimilarityAnalyzer: analyze similarity between two molecule sets

    • PropertyPlotter: plot molecule properties

    • RMSDCalculator: calculate RMSD between conformations

    • VendorFinder: search vendors for compounds

    Convert, combine and store:

    • DockResultMerger: merge docking output files and/or filter them

    • MolCombine: combine molecular files

    • DBImporter: import molecules into DB

    • Converter: interconvert molecular file-formats

    • MolDepict: generate structure diagrams

    • VendorFinder: search vendors for compounds

    For more information about an individual tool, please call the tool without any parameters (or with ‘-help’).

     

     

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