| This package contains tools belonging to
CADDSuite: A flexible and open framework for Computer-Aided Drug Design For more information, please go to http://caddsuite.github.com There are tools for the following tasks: Get Data: - CombiLibGenerator: generate R-group decorated ligands - DBExporter: fetch (filtered) molecules from DB Preparation of input: - 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 Off-target search: - PocketCutter: cut binding pocket surface - SurfaceMatcher: match two protein surfaces onto each other 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 |
hg clone https://toolshed.g2.bx.psu.edu/repos/marcel/caddsuite_linux_x86_64