annotate CADDSuite-1.5/CADDSuite-description.txt @ 15:ac342506cd4e draft

CADDSuite version 1.5

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
	- PocketCutter: cut binding pocket surface
	- SurfaceMatcher: match two protein surfaces onto each other
	- 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').