Cell Directory

Directory of cells available in Squonk. You can filter by any of the terms in the table.

Further information about usage is available from page describing the cell.

Entries

Page nameCategorySourceDescription
3DMol.jsVisualAcademic Open SourceStructure 3D viewer, allowing proteins and ligands to be displayed and manipulated. Uses 3DMol.js from University of Pittsburgh
Atom Count (CXN)Molecular PropertiesChemAxonAtom count calculator for structures using ChemAxon's property calculators
Box PlotVisualSquonkDisplays data as a box plot using the D3 Javascript library
CNS MPO (CXN)Molecular PropertiesChemAxonMulti-Parameter Optimisation score for drugs targeted at the Central Nervous Systmem (CNS).
CSV UploadInput/OutputSquonkAllows a text file to be uploaded into the system. Comma and tab separated formats are supported along with basic options like whether to handle first line as headers.
Canonical Smiles (RDKit)Molecular PropertiesRDKitGenerate a canonical smiles string for structures using RDKit
ChEMBL Activities FetcherInput/OutputEBIPulls compound and activity data for a specified assay ID from the ChEMBL REST web services at the EBI
Chemcentral Similarity SearchStructure searchRDKitSearch our "house" databases using similarity search
Chemcentral Structure SearchStructure searchRDKitSearch our "house" databases using exact or substructure search
Chemcentral multi-searchStructure searchRDKitSearch our "house" databases to find structures similar to any of the input structures
Convert to MoleculesTransformSquonkGenerate molecules from text representation e.g. a smiles column from a CSV file
Dataset Docker ProcessorProgrammingSquonkProcess a dataset using a specified Docker container
Dataset EnricherTransformSquonkEnriches one dataset with content from another
Dataset PotionTransformSquonkA simple language for performing powerful data transformations
Dataset Random SelectorFilterSquonkSelect records at random from a dataset
Dataset UUID filterFilterSquonkFilter a dataset with a set of UUIDs
Dataset slice selectorFilterSquonkSimple cell that let's you prepare a subset of a large dataset starting at a specified entry and including a specified number of entry
Dataset sorterTransformSquonkSort a dataset by one or more fields
Drug-like Filter (CXN)Molecular PropertiesChemAxonApply a drug likeness filter to molecules using ChemAxon's property calculators
ECFP4 Screen (CXN)Molecular ScreeningChemAxonFilter molecules with ECFP fingerprints similarity using ChemAxon's Screen
Formal Charge (RDKit)Molecular PropertiesRDKitCalculates the formal charge of a molecule. e.g. 1+, 2+, 1-, 0 (for neutral)
Frac sp3 C (RDKit)Molecular PropertiesRDKitCalculate the fraction of sp3 hybridised carbon atoms for structures using RDKit
Ghose filter (CXN)Molecular PropertiesChemAxonGhose drug like filter implemented with ChemAxon's property calculators
Ghose filter (RDKit)Molecular PropertiesRDKitGhose drug like filter implemented using RDKit
Groovy Dataset FilterFilterSquonkFilter a dataset based on an expression using the Groovy programming language.
HBA & HBD (CDK)Molecular PropertiesCDKH-bond acceptors and donors using Chemistry Development Kit
HBA & HBD (RDKit)Molecular PropertiesRDKitCalculate the number of h-bond donors and acceptors for structures using RDKit
HeatmapVisualSquonkDisplay of relationships between data using a heatmap
Image ViewerVisualSquonkSimple viewer for image files
KiDS MPO (CXN)Molecular PropertiesChemAxonMulti-Parameter Optimisation score for kinase drugs.
Lipinski filter (CXN)Molecular PropertiesChemAxonLipinski filter for structures using ChemAxon's property calculators
Lipinski filter (RDKIT)Molecular PropertiesRDKitCalculate Lipinski properties for structures using RDKit
LogD (CXN)Molecular PropertiesChemAxonLogD predictor for structures using ChemAxon's property calculators
LogP (CDK)Molecular PropertiesCDKALogP and XLogP predictors for structures using Chemistry Development Kit
LogP (CXN)Molecular PropertiesChemAxonLogP predictor for structures using ChemAxon's property calculators
LogP (OpenChemLib)Molecular PropertiesOpenChemLibLogP predictor for structures using OpenChemLib
LogP (RDKit)Molecular PropertiesRDKitPredict LogP using RDKit
LogS (CXN)Molecular PropertiesChemAxonLogS (solubility) predictor for structures using ChemAxon's property calculators
LogS (OpenChemLib)Molecular PropertiesOpenChemLibSolubility (LogS) predictor for structures using OpenChemLib
Merge DatasetsTransformSquonkMerge multiple datasets into one using a common key. Useful for combining data from multiple sources into a single dataset where there is a common identifier linking the records
MolAlignAssembliesMolecular ScreeningOtherAlignment of 3D structures
Molar Refractivity (RDKit)Molecular PropertiesRDKitPredict molar refractivity using RDKit
Molecule standardisersTransformRDKitTwo cells performing molecular standardisation using the MolVS and Flatkinson standardisers.
MoleculeEnumeratorTransformRDKitEnumerates potential variants of a structure using RDKit
Molecules From FieldInput/OutputSquonkCreates a new dataset containing molecules present in the specified field of the input.
Molfile UploadInput/OutputSquonkAllows a dataset to be created from a file in molfile format. The dataset will contain a single structure.
NGL ViewerVisualPDB/RCSBNGL 3D viewer from Alexander Rose
PAINS filter (RDKit)Molecular PropertiesRDKitFilter molecules using PAINS (Pan Assay Interference Compounds) filters, implemented with RDKit
PDB UploadInput/OutputSquonkAllows file in PDB format to be uploaded
PLI score3DCommercial Open SourceScores docked structures using the Astex PLI scoring algorithm.
PSA (OpenChemLib)Molecular PropertiesOpenChemLibCalculate the polar surface area for structures using OpenChemLib
Parallel Coordinate PlotVisualSquonkDisplay and filter data using a parallel coordinate plot
Pharmacophore Screen (CXN)Molecular ScreeningChemAxonFilter molecules with a 2D pharmacophore similarity using ChemAxon's Screen
RDKit Butina ClusteringClusteringRDKitCluster molecules using the Butina algorithm from RDKit.
RDKit Cluster MatrixClusteringRDKitGenerates a clustered distance matrix from a dataset of molecules using Butina clustering from RDKit.
RDKit ConformersMolecular PropertiesRDKitGenerate 3D conformers of molecules using RDKit
RDKit Constrained ConformersMolecular PropertiesRDKitGenerate conformers of a molecule, constraining a part of a molecule to fixed coordinates.
RDKit Diverse Subset PickerClusteringRDKitCluster molecules using the Butina algorithm from RDKit and then pick a diverse subset of the molecules
RDKit MaxMin PickerClusteringRDKitPicks diverse subset of compounds using the MaxMinPicker algorithm as implemented in RDKit
RDKit Multi-Similarity ScreeningMolecular ScreeningRDKitVirtual screening using molecular similarity
RDKit Open3D AlignMolecular ScreeningRDKitPerforms 3D alignment of molecules using Open3DAlign
RDKit Similarity ScreeningMolecular ScreeningRDKitVirtual screening using molecular similarity
REOS Filter (RDKit)Molecular PropertiesRDKitRapid Elimination Of Swill filter - a drug-like structure filter using RDKit
REOS filter (CXN)Molecular PropertiesChemAxonApply a drug likeness filter to molecules using ChemAxon's property calculators
Ring Count (RDKit)Molecular PropertiesRDKitCalculate the number of rings and aromatic rings for structures using RDKit
Rotatable bonds (RDKit)Molecular PropertiesRDKitCalculate the number of rotatable rings for structures using RDKit
Rule of 3 filter (CXN)Molecular PropertiesChemAxonAstex rule of 3 filter for filtering fragment libraries implemented with ChemAxon
Rule of 3 filter (RDKit)Molecular PropertiesRDKitAstex rule of 3 filter for filtering fragment libraries implemented with RDKit
SDF Export (CDK)Input/OutputCDKExport structures to SDF using Chemistry Development Kit
SDF UploadInput/OutputSquonkAllows a MDL SD file to be uploaded into the system. Structures and data are handled.
SMARTCypMolecular PropertiesAcademic Open SourceSMARTCyp metabolic site prediction
SMoG20163DAcademic Open SourceScores docked structures using the SMoG 2016 scoring algorithm.
Scatter PlotVisualSquonkDisplays data as a scatter plot using the D3 Javascript library
Smiles StructuresInput/OutputSquonkRead structures from smiles strings
Smiles deduplicatorFilterSquonkDe-duplicate a set of structures using a canonical smiles field
SphereEx Clustering (CXN)ClusteringChemAxonCluster molecules using sphere exclusion clustering and ECFP fingerprints using ChemAxon's JKulstor
TPSA (RDKit)Molecular PropertiesRDKitCalculate topological polar surface area for structures using RDKit
Table DisplayVisualSquonkDisplays data as a familiar table/spreadsheet
Tmax Cmax SimulationDMPKOtherSimulator for Pharmacokinetic profiling of a compound
Transform ValuesTransformSquonkConvert data types e.g. convert from text to numbers
Trusted Groovy ScriptProgrammingSquonkProcess a dataset using a Groovy script. The script is trusted and executed "in process"
Untrusted Groovy ScriptProgrammingSquonkProcess a dataset using a Groovy script. The script is not trusted and executed in its own safe sandbox.
Veber filter (CXN)Molecular PropertiesChemAxonVeber filter for orally active drugs implemented using ChemAxon
Veber filter (RDKit)Molecular PropertiesRDKitVeber filter for orally active drugs implemented using RDKit
Verify structure (CDK)Input/OutputCDKVerify that the molecules are valid according to CDK
Verify structure (CXN)Input/OutputChemAxonVerify that the molecules are valid according to ChemAxon's Marvin
Verify structure (OCL)Input/OutputOpenChemLibVerify that the molecules are valid according to OpenChemLib
Verify structure (RDKit)Input/OutputRDKitVerify that the molecules are valid according to RDKit
Wiener Numbers (CDK)Molecular PropertiesCDKWiener path and polarity numbers using Chemistry Development Kit
XChem Reaction MakerTransformRDKitEnumerate input molecules using a specified reaction and some reactions
XChem Reaction Smarts FilterMolecular ScreeningRDKitFilter a set of molecules according to whether they contain a substructure fragment compatible with a set of reaction types
ZipFileUploadInput/OutputSquonkCell that allows a zip file to be uploaded.
pKa (CXN)Molecular PropertiesChemAxonAcidic and basic pKa predictors using ChemAxon's property calculators
rDock Docking3DCommercial Open SourceLigand docking using rDock