tool_list

List of ballaxy tools

A relatively updated list can be found on our preinstalled server at https://ballaxy.bioinf.uni-sb.de. If you have feature requests or even created tools that you want to make available for others please don't hesitate to contact our developer team.

topic	tool	aim
Get Data	Upload File from your computer	The system will attempt to detect mol, mol2, pdb, sdf, ac, hin, and xyz formats. If your file is not detected properly as one of the known formats, it most likely means that it has some format problems. You can still coerce the system to set your data to the format you think it should be.
	PDBDownload	Download a PDB entry from the Protein Data Bank (http://www.pdb.org/) using the specified ID of the desired database entry.
	MolecularFileConverter	This tool can be used to convert between different molecular file-formats.
	Split2ConnectedComponents	This tool splits a given molecular file into its connected components. Output of this tool is a number of mol2 files each containing one connected component.
	PDBCutter	This tool splits a given PDB file into receptor and reference ligand, respectively. Optionally, chains (e.g. in case of multimers) or specified residues (e.g. water or ions) that you don't need can be deleted. Output of this tool is one PDB file containing the receptor, i.e. the protein w/o reference ligand and w/o undesired chains/residues, and one PDB file containing the reference ligand.
	LigandFileSplitter	This tool splits a single multi-molecule file into multiple (multi)-molecule files. The splitting behaviour can be controlled by defining the number of output files or the maximum number of molecules per output file.
	MolCombine	This tool generates the intersection or union of two multi-molecule input files. Comparison is performed on molecule basis.
	EvenSplit	This tool splits a molecule file into two subsets a way that each of them covers an equal range of a specified target property.
	MolFilter	This tool can filter molecules from a molecule input file according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s). Output of this tool is a molecule file that contains all compounds that match all specified search criteria.
	CombiLibGenerator	This tool generates a combinatorial library by combining the given molecule scaffolds with possible combinations of moieties. Output of CombiLibGenerator is a file containing created topologies. Note that this tool does not generate any conformations. All coordinates in the output file will be zero.
	DBImporter	This tool imports molecules into a database.
	DBExporter	This tool exports compounds from a database to a molecular file. Compounds can be filtered according to SMARTS expressions, logP, molecular weight, or similarity to query molecule(s) and dataset name.
	VendorFinder	This tool can be used to fetch information about vendors for each compound in the given input file from a user created data base.
Structure Creation	PeptideBuilder	This tool creates a peptide by a given torsion file. The amino acids shall be given in three letter code, the phi, psi, and omega angles shall be given in degree.
	Create Molecule from SMILES	This tool creates a molecule in mol2 format from a given SMILES expression.
	CrystalGenerator	This tool creates crystals given a asymetric unit and a space group.
Force Field	ResidueChecker	This tool check residues to debug a protein structure wrt to PDB conventions.
	CalculateBindingFreeEnergy	This tool calculates the binding energy of two proteins using AMBER.
	CalculateSolvationFreeEnergy	This tool calculates the solvation free energy of a protein using AMBER .
	CalculateEnergy	This tool calculates the free energy of a protein.
Preparation	AddMissingAtoms	This tool allows you to add missing hydrogens to a protein structure. Output of this tool is a PDB file containing the input protein structure with added hydrogens.
	ProteinProtonator	This tool allows you to protonate a protein structure in a pH dependent manner. Output of this tool is a PDB file containing the protonated input protein structure.
	BondOrderAssigner	This tool computes bond order assignments for a given ligand based on a valence-based scoring function (BALL or Antechamber)
	Ligand3DGenerator	This tool takes input compounds and generates a single 3D conformation for each molecule, which is ready for docking.
	WaterFinder	This tool searches for crystal waters that either interact strongly with the receptor or that interact strongly with receptor and reference ligand, thus functioning as a water bridge. Output of this tool is a PDB file containing the protein and all strongly bound water molecules.
	PartialChargesCopy	This tool copies partial charges from a given molecule file to the conformations read from a different file. This can be useful when computing partial charges with external tools.
	PropertyModifier	With this tools you can add, rename or delete molecule property tags.
	BindingDBCleaner	This tool cleans up the SD file properties downloaded from bindingdb.org. For all compounds in the input file, the affinity value for the specified target is searched and retained but all other properties are removed. Furthermore, the IC50 or Ki value of each compound is converted to a binding-free-energy value in units of [kJ/mol] that is added as a property-tag named 'binding_free_energy'. All compounds in the input file for which no IC50 resp. Ki value for the specified target can found, are ignored and not written to the output file.
BOA Constructor	MolecularFileConverter	This tool can be used to convert between different molecular file-formats.
	BondOrderAssigner	This tool computes bond order assignments for a given ligand based on a valence-based scoring function (BALL or Antechamber)
	Split2ConnectedComponents	This tool splits a given molecular file into its connected components. Output of this tool is a number of mol2 files each containing one connected component.
!Graph/Display Molecules	Structure Diagram	This tool creates a structure diagram of a given ligand molecule.
Checks and evaluations	LigCheck	This tool checks all molecules of the given input file for errors. The following properties are checked to have meaningful values: bond-lengths, single fragment, valid elements, protonation, 3D coordinates, partial charges.
	ProteinCheck	Check a given protein structure for the following errors: bond-lengths, single fragment, valid elements, protonation, 3D coordinates, temperature factors, steric clashes. A protein structure quality report, containing the results of those tests and a secondary structure prediction, a Ramachandran plot and a temperature factor plot will be generated and saved as a PDF file.
Analysis	PropertyPlotter	This tool can be used to generate distribution- or scatter-plots of data contained in molecule property-tags. The output of this tool is a plot in form of an EPS or PNG file.
	PDBRMSDCalculator	This tool computes the RMSD between proteins. Output of this tool is a either the rmsd (in case of binary PDB comparison) or an output file containing the RMSD between the first pose and all other poses.
	RMSDCalculator	This tool calculates the RMSD between different conformations of the same molecule. It can be used to evaluate the differences between ligand poses taken from co-crystal structures, e.g. generated by a docking run. Output of this tool is a molecule file which will for each molecule contain a new property-tag 'RMSD' with the calculated RMSD value.
	ScoreAnalyzer	This tool can be used generate plots that allow to evaluate the quality of docking or (re-)scoring. The type of plot to be generated must be chosen by either '-roc', '-top50', '-scatter' or '-enrichment'. The output of this tool is a plot in EPS or PNG format.
	SimilarityAnalyzer	This tool evaluates the 2D fingerprint (tanimoto) similarity between molecules in two input files and creates a distribution plot to visualize the result. The resulting plot (in form of an eps-, png- or pdf-file; as chosen) shows the distribution of similarity values obtained by comparing each molecule in input file 1 against each molecule in input file 2.
Docking	PocketDetector	This tool tries to detect the binding pocket in which the reference ligand is located. Output of this tool is a docking configuration file that contains the description of the detected binding pocket, which can be used in further docking steps.
	ConstraintsFinder	This tool searches protein residues with which the reference ligand strongly interacts. Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.
	InteractionConstraintDefiner	This tool allows to define interaction constraints for docking or scoring. The constraint to be created will enforce a specified minimal interaction between ligands and the specified residue(s) of the receptor. Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.
	SpatialConstraintDefiner	This tool allows to define spatial constraints for docking or scoring. Output of this tool is a docking configuration file containing the created constraints. This file should in following pipeline steps be specified for grid precalculation and docking.
	GridBuilder	This tool precalculates a score-grid for a binding pocket of a given receptor. Output of this tool is a file containing the score-grids that can be used by docking-/scoring-tools of BALL (e.g. IMGDock).
	IMGDock	This tool is BALL's docking engine. IMGDock docks compounds into the binding pocket of a receptor using an iterative multi-greedy approach.
	DockResultMerger	This tool can be used to combine output files from multiple (e.g., parallel) docking runs.
Rescoring	SimpleRescorer	This tool rescores docking poses. A scoring function is used to evaluate the binding-free-energy of each compound. This is similar to the scoring done during docking; details depend on the specified config-file. Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.
	AntitargetRescorer	This tool rescores docking poses and tries to enhance target specificity. Compounds that were docked into the target and into unrelated proteins have to be supplied here. All compounds that received a very good antitarget-score will be penalized, i.e. they will have a much worse score within the output file. Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 'antitarget_rescore'.
	TaGRes	This tool rescores docking poses using Target-specific Grid-Rescoring. It is based on a regression model for binding-affinity approximation for your target which has been generated by the tool TaGRes-train. TaGRes will evaluate each given input pose with a scoring function and apply the specified regression model to the score contributions generated this way, resulting in a re-score value, i.e. a (probably) enhanced approximation of the compound's binding-free-energy. Output of this tool is a file in the same format as the input ligand file containing all compounds with scores obtained by rescoring in form of a property 're-score'.
	TaGRes-train	This tool generates a model for Target-specific Grid-Rescoring (TaGRes).
	SLICK	This tool provides access to BALL's carbohydrate-specififc scoring function.
NMR NightShift	...
Clustering		The following tools are based on our publication "Efficient computation of root mean square deviations under rigid transformations" in the Journal of Computational Chemistry 2014
	Trajectory2RigidTransformation	This tool converts a trajectory file into a rigid transformation file, which is needed for the DockPoseClustering tool.
	PDBRMSDCalculator	This tool computes the RMSD between protein poses. Output of this tool is a either the RMSD (in case of binary PDB comparison) or an output file containing the RMSD between the first pose and all other poses.
	DockPoseClustering	This tool clusters docking poses given a conformation set or a list of rigid transformations. Available algorithms for clustering are: CLINK_DEFAYS, NEAREST_NEIGHBOR_CHAIN_WARD, SLINK_SIBSON, or TRIVIAL_COMPLETE_LINKAGE. Optional parameters are the the minimal rmsd between the final clusters, the rmsd type (SNAPSHOT_RMSD, RIGID_RMSD, CENTER_OF_MASS_DISTANCE), and the type of atoms used for scoring a pose.
	ExtractClustersFromWardTree	This tool extracts docking clusters from a cluster index Ward tree produced by the tool DockPoseClustering.
	TrajectoryFile2PDBSplitter	This tool splits SnapShots into PDB files. This is a preparatory tool for DockPoseClustering.
	PoseIndices2PDB	This tool converts pose indices produced by e.g. the tool DockPoseClustering back into PDB files.
QuEasy (QSAR)	InputReader	This tool reads input from SD file and generate features for QSAR analysis. A property tag containing the response value has to be specified. The tool calculates a set of standard descriptors but also accepts input of additional descriptors.
	InputPartitioner	This tool partitions a given QSAR data set into n partitions with evenly distributed response values. Thus, this tool can be useful as part of a nested validation pipeline. Input is a data file as generated by InputReader and the output consists of multiple (n) files.
	ModelCreator	This tool creates a QSAR model using an input data set as generated by InputReader. The type of QSAR model can be be specified. Optimization of model- and kernel-parmeters will be done automatically using cross-validation. Output of this tool is a model-file that can be used by other QSAR tools.
	AutoModel	This tool tries to automatically find the best QSAR model for a given data set. It therefore applies nested validation, including feature selection, for each available model-type. The model with the best nested prediction quality is saved to the specified output file.
	Validator	Validator evaluates the quality of a QSAR model. The validation technique can be selected.
	FeatureSelector	This tool runs a feature-selection for a given QSAR model. The type of feature-selection can be specified. Input of this tool is a data file as generated by InputReader containing the training data for feature-selection and a QSAR model file as generated by ModelCreator. Output of this tool is a model-file that can be used by other QSAR tools.
	Predictor	This tool predictes the response values of compounds in the given data-file using the specified QSAR model. Output of this tool is a text file containing the predicted and, if any, the expected response values.
	MolPredictor	This tool predictes the response values of compounds in the given molecule file using the specified QSAR model. Features for all molecules in the input file are generated automatically. Output of this tool is a molecule file containing the predicted values as a property tag named 'predicted_activity'.
Chemoinformatics	FingerprintSimilaritySearch	This tool performs a cutoff similarity search of compounds in a query file against all compounds in a target file. The compounds have to be encoded as 2D binary fingerprints either as a binary string or comma-separated list of integer features. The output file will contain all entries from the target file that exceed the similarity cutoff for at least one molecule from the query file.
	FingerprintSimilarityClustering	This tool performs a clustering of all compounds in an input. The compounds have to be encoded as 2D binary fingerprints either as a binary string or comma-separated list of integer features. The clustering procedure combines connected component decomposition of a tanimoto similarity network followed by average linkage hierarchical clustering. A cluster selection level is automatically chosen and the output file contains the cluster ID for every compound.