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1 This package contains tools belonging to
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2 CADDSuite: A flexible and open framework for Computer-Aided Drug Design
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3
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4 There are tools for the following tasks:
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5
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6 Get Data:
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7 - CombiLibGenerator: generate R-group decorated ligands
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8 - DBExporter: fetch (filtered) molecules from DB
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9
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10 Preparation of input:
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11 - PDBCutter: separate ligand and receptor
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12 - ProteinProtonator: protonate protein structures
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13 - BindingDBCleaner: fix data from bindingdb.org
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14 - EvenSplit: generate splits w/ equal property range
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15 - PropertyModifier: modify property tags
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16 - LigandFileSplitter: split molecule files
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17 - Ligand3DGenerator: generate 3D coordinates for small molecules
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18
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19 Structure checks and evaluations:
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20 - ProteinCheck: evaluate protein quality
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21 - LigCheck: chemical sanity check for ligands
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22
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23 QuEasy (QSAR):
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24 - InputReader: read molecules and generate features
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25 - ModelCreator: create a QSAR model
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26 - FeatureSelector: automatically select features of a QSAR model
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27 - Validator: evaluate quality of a QSAR model
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28 - MolPredictor: predict molecule activities with QSAR model
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29 - AutoModel: automatically find best QSAR model
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30
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31 Docking:
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32 - WaterFinder: find strongly bound water molecules
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33 - SpatialConstraintDefiner: define spatial constraint
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34 - InteractionConstraintDefiner: define interaction constraint
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35 - ConstraintsFinder: find strongly interacting residues
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36 - PocketDetector: detect ligand binding pocket
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37 - GridBuilder: precalculate grids for docking
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38 - IMGDock: run Iterative Multi-Greedy Docking
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39
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40 Rescoring:
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41 - SimpleRescorer: rescore docking results
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42 - TaGRes-train: Target-specific Grid-Rescoring, training
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43 - TaGRes: Target-specific Grid-Rescoring
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44 - AntitargetRescoring: rescore w/ respect to antitarget
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45
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46 Analysis:
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47 - ScoreAnalyzer: generate ROC or enrichment plots
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48 - SimilarityAnalyzer: analyze similarity between two molecule sets
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49 - PropertyPlotter: plot molecule properties
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50 - RMSDCalculator: calculate RMSD between conformations
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51 - VendorFinder: search vendors for compounds
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52
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53 Convert, combine and store:
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54 - DockResultMerger: merge docking output files and/or filter them
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55 - MolCombine: combine molecular files
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56 - DBImporter: import molecules into DB
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57 - Converter: interconvert molecular file-formats
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58 - MolDepict: generate structure diagrams
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59 - VendorFinder: search vendors for compounds
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60
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61 For more information about an individual tool, please call the tool without any parameters (or with '-help').
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