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comparison CADDSuite/CADDSuite-description.txt @ 0:8ce0411aaeb3

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Uploaded CADDSuite version 0.94
author marcel
date Sun, 26 Jun 2011 14:01:09 -0400
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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 - SpatialConstraintDefiner: define spatial constraint
34 - ConstraintsFinder: find strongly interacting residues
35 - PocketDetector: detect ligand binding pocket
36 - GridBuilder: precalculate grids for docking
37 - IMeedyDock: run Iterative Multi-Greedy Docking
38
39 Rescoring:
40 - SimpleRescorer: rescore docking results
41 - TaGRes-train: Target-specific Grid-Rescoring, training
42 - TaGRes: Target-specific Grid-Rescoring
43 - AntitargetRescoring: rescore w/ respect to antitarget
44
45 Analysis:
46 - ScoreAnalyzer: generate ROC or enrichment plots
47 - SimilarityAnalyzer: analyze similarity between two molecule sets
48 - PropertyPlotter: plot molecule properties
49 - RMSDCalculator: calculate RMSD between conformations
50 - VendorFinder: search vendors for compounds
51
52 Convert, combine and store:
53 - DockResultMerger: merge docking output files and/or filter them
54 - MolCombine: combine molecular files
55 - DBImporter: import molecules into DB
56 - Converter: interconvert molecular file-formats
57 - MolDepict: generate structure diagrams
58 - VendorFinder: search vendors for compounds
59
60 For more information about an individual tool, please call the tool without any parameters (or with '-help').