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Chain tools into multi-step pipelines—start from a template or build your own.

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Computational Biology

Modeling and analysis tools for biomolecular research

AutoDock VinaHigh performance molecular docking and virtual screening for drug discoveryBinding-Site DetectorFind ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflowsBoltz-2Accurate in silico screening for early-stage drug discoveryBoltzGenDesign proteins and peptides to bind biomolecular targetsDiffDockProtein-ligand docking with diffusion models and confidence-ranked posesDrugFlowGenerate candidate ligands from a protein target and reference ligand using flow matchingESMFold2Predict protein, DNA, RNA, and ligand complex structures with evolutionary scale modelingEvo 2Genome modeling and design across all domains of life with the Evo 2 DNA language modelFreeBindCraftDesign miniprotein and peptide binders against a target structure using open-source scoringGNINACNN-accelerated protein–ligand docking and rescoringInteraction ProfilerEnumerate hydrogen bonds, hydrophobics, salt bridges, and π-stacking in docked complexesMD Trajectory AnalyzerCompute RMSD, Rg, RMSF, ligand H-bond occupancy, and representative frames from OpenMM trajectoriesMM-GBSA RescoringEnd-point implicit-solvent MM-GBSA rescoring of docked poses or protein–ligand complexesOpenDDEPredict protein, nucleic acid, and small-molecule complex structures with OpenDDEOpenMM MDPrepare, solvate, and equilibrate protein structures with OpenMM molecular dynamicsProtein PreparerPDBFixer cleanup, PDB2PQR protonation, and dock-ready structures without MD solvationRFAntibodyAntibody and TCR design with RFdiffusion, ProteinMPNN, and RF2 (stages or full pipeline)Sequence MutatorApply point mutations such as T315I to a protein sequence, checking each wild-type residueSurfDockSurface-informed diffusion docking with a reference-ligand pocket and screen-model rescoringSURFMAP2D projections of protein surface features from PDB structures or SURFMAP matrix filesThompson SamplingActive-learning virtual screening of un-enumerated combinatorial libraries via Thompson Sampling

Cheminformatics & Structure

General-purpose tools for working with molecular structures and data

3D Shape Similarity3D shape and pharmacophore virtual screening: rank libraries against a query conformer with USRCAT and Gaussian shape + color overlay to find scaffold hopsADMET PredictorPredict 41 ADMET endpoints (solubility, permeability, CYP, hERG, toxicity) from SMILES with pretrained Chemprop modelsBioactivity Dataset Curator & SplitterNormalize assay units, censoring, and replicates into SAR/QSAR datasets with scaffold, random, or time splitsChEMBL Target ActivitiesPull measured IC50, Ki, Kd and EC50 values for your targets from ChEMBL into one table, ready to curate and train onConformer Ensemble GeneratorGenerate an RDKit 3D conformer ensemble per molecule (energy window / RMSD prune)Drug-likeness & Structural AlertsScore and filter molecules with Lipinski, Veber, QED, SA score, and PAINS/Brenk/NIH alertsFingerprint Similarity & ClusteringTanimoto nearest neighbors, Butina clustering, MaxMin diversity, and Scanpy PCA/UMAP/Leiden clustering from molecular fingerprintsFree Wilson AnalysisQuantify R-group SAR contributions and predict unsynthesized molecules from activity dataImage to Structure (OCSR)Read chemical structures and reaction schemes from images of papers, slides and whiteboards as SMILES, with each reading checked by a second modelMatched Molecular PairsHussain–Rea matched pairs: chemical transforms and activity deltas from a SMILES libraryMetabolite EnumeratorPredict ranked phase I and phase II metabolite structures with parent and pathway provenanceMolecule ConversionConvert molecule file/data formatMolecule StandardizerSalt-strip, neutralize, tautomer, and stereo cleanup to parent structuresMolGenGenerate novel, chemically valid analogs of a seed molecule with a SELFIES molecular language modelPaDEL-DescriptorCalculate molecular descriptors and fingerprintsReaction Atom MapperAtom-map reaction SMILES and check element, charge, and stereochemistry balanceReaction EnumerationEnumerate product libraries from reaction SMARTS or RXN files and reactant SMILES listsRetrosynthesisPropose ranked one-step or short-route retrosynthetic disconnections and building blocks from target SMILESRMSD CalculatorCalculate the root-mean-square deviation (RMSD) of moleculesScaffold AnalyzerInventory Bemis–Murcko scaffolds, frequencies, and one representative per scaffold from a SMILES librarySmall-Molecule Force-Field ParameterizerAssign OpenFF Sage force-field parameters and partial charges to small molecules as reusable, validated systemsStereoisomer EnumeratorExpand unassigned stereocenters and E/Z double bonds into explicit stereoisomers with a parent-to-isomer auditStructure VisualizerInteractive 3D viewer for proteins, complexes, and small molecules

Quantum Chemistry

Electronic structure, vibrational spectra, and related quantum chemical analysis

PySCF Electronic StructureHartree–Fock, DFT, TDDFT, optimization, frequencies, and charges with PySCF / GPU4PySCFQiskit SQDActive-space ground-state energies by sample-based quantum diagonalization on the Qiskit Aer simulatorVibrational Spectrum LibraryGFN2-xTB IR spectra for every conformer of an ensemble, broadened onto a shared wavenumber grid with Boltzmann-weighted ensemble spectraxTB / CRESTGFN2-xTB and GFN-FF energies, optimizations, and IR frequencies, plus CREST conformer, tautomer, and protomer ensembles

Fluids & Thermodynamics

Chemical kinetics, phase equilibrium, thermodynamics, and transport simulations

Adsorption Isotherm AnalyzerFit Langmuir, Toth, and Sips isotherms, BET areas, isosteric heats, and IAST mixture uptakes to rank porous adsorbentsCanteraChemical kinetics, thermodynamics, and transport simulations for combustion and reacting flowsCoolPropOpen CoolProp / IAPWS real-fluid properties: steam tables, refrigerants, and two-phase Helmholtz EOSGroup-Contribution PropertiesEstimate Joback and Crippen properties from SMILES for VLE, thermo, and Cantera workflowsHansen Solubility ParametersEstimate Hansen δD/δP/δH from SMILES and rank solvents by HSP distance, RED, and Flory–Huggins χKinetic Parameter FitterFit rate constants and Arrhenius parameters to concentration–time data and emit a Cantera YAML mechanismMechanism ReductionReduce a detailed kinetic mechanism to a skeletal Cantera YAML with pyMARS DRGEP / DRG / PFA against ignition-delay and flame-speed targetsNASA / Cantera Species BuilderFit NASA-7 polynomials from a Cp(T) table or Joback properties and emit a Cantera YAML species fragmentPHREEQC Aqueous SpeciationAqueous speciation, titration, and mixing with USGS PHREEQC for electrolytes and mineral saturationReaction Calorimetry & Thermal-Safety ModelSimulate batch or semi-batch reaction heat balances and screen thermal runaway with MTSR, adiabatic rise, and TMR_adRMG Mechanism GeneratorGenerate Chemkin / Cantera reaction mechanisms with RMG-Py from species, T/P, and terminationSolid–Liquid Equilibrium / Eutectic DiagramBinary liquidus curves, eutectic point, and solubility versus temperature with ideal, NRTL, or UNIFAC activityTransition-State-Theory Rate CalculatorCompute Eyring TST rate constants over a temperature grid from activation or species thermochemistry and fit Arrhenius parametersVLE / FlashMulticomponent vapor–liquid phase equilibrium with cubic EOS and UNIFAC or NRTL activity modelsVLE Parameter RegressionFit binary NRTL interaction parameters to measured Txy or Pxy vapor–liquid equilibrium dataVLE Thermodynamic Consistency CheckerAudit binary Txy or Pxy vapor–liquid equilibrium data with Gibbs–Duhem area, point, endpoint, and infinite-dilution tests

Custom Modeling

Train and run your own structure–property models. Manage saved models in My Models.

MPNN ModelsFast structure-property inference that highlights key molecule substructuresPython Script SandboxShort RDKit, pandas, NumPy and SciPy analyses of your results, run in isolation with no network accessQSAR ModelsCompare random forest, LightGBM, Gaussian process and other QSAR models on your data and keep the bestReaction ModelsPredict reaction yield, selectivity and rates from atom-mapped reactions and their conditionsThermo Property ModelsCorrect Joback and Hansen estimates with your own measurements, and predict solubility and mixture properties across solvents and temperatures