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