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comparison CADDSuite/CADDSuite-description.txt @ 0:bac3c274238f

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Migrated tool version 0.93 from old tool shed archive to new tool shed repository
author marcel
date Tue, 07 Jun 2011 16:43:30 -0400
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children 867bf9f815a0
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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 - ConstraintsFinder: find strongly interacting residues
34 - PocketDetector: detect ligand binding pocket
35 - GridBuilder: precalculate grids for docking
36 - IMeedyDock: run Iterative Multi-Greedy Docking
37
38 Rescoring:
39 - SimpleRescorer: rescore docking results
40 - TaGRes-train: Target-specific Grid-Rescoring, training
41 - TaGRes: Target-specific Grid-Rescoring
42 - AntitargetRescoring: rescore w/ respect to antitarget
43
44 Analysis:
45 - ScoreAnalyzer: generate ROC or enrichment plots
46 - SimilarityAnalyzer: analyze similarity between two molecule sets
47 - PropertyPlotter: plot molecule properties
48 - RMSDCalculator: calculate RMSD between conformations
49 - VendorFinder: search vendors for compounds
50
51 Convert, combine and store:
52 - DockResultMerger: merge docking output files and/or filter them
53 - MolCombine: combine molecular files
54 - DBImporter: import molecules into DB
55 - Converter: interconvert molecular file-formats
56 - MolDepict: generate structure diagrams
57 - VendorFinder: search vendors for compounds
58
59 For more information about an individual tool, please call the tool without any parameters (or with '-help').