CADDSuiteTools

The CADDSuite tools can be found at

ball/build/bin/TOOLS/<tool name>

if you followed the build instructions.

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