Mercurial > repos > marcel > caddsuite_linux_x86_64
diff CADDSuite-1.0.1/CADDSuite-description.txt @ 9:2cff9609f2c7
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author | marcel |
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date | Tue, 15 Nov 2011 10:40:26 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CADDSuite-1.0.1/CADDSuite-description.txt Tue Nov 15 10:40:26 2011 -0500 @@ -0,0 +1,61 @@ +This package contains tools belonging to +CADDSuite: A flexible and open framework for Computer-Aided Drug Design + +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 + +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').