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Tools
What each tool computes, its inputs and outputs, and how it is priced.
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Computational Biology
- Boltz-2Accurate in silico screening for early-stage drug discoveryboltz2
- BoltzGenDesign proteins and peptides to bind biomolecular targetsboltzgen
- DiffDockProtein-ligand docking with diffusion models and confidence-ranked posesdiffdock
- DrugFlowGenerate candidate ligands from a protein target and reference ligand using flow matchingdrugflow
- Sequence MutatorApply point mutations such as T315I to a protein sequence, checking each wild-type residuesequence-mutate
- ESMFold2Predict protein, DNA, RNA, and ligand complex structures with evolutionary scale modelingesmfold2
- Evo 2Genome modeling and design across all domains of life with the Evo 2 DNA language modelevo2
- AutoDock VinaHigh performance molecular docking and virtual screening for drug discoveryautodockvina
- Binding-Site DetectorFind ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflowspocket-detect
- Docking Protocol ValidatorRedock co-crystallized ligands and score pose RMSD and enrichment to validate a docking setup before screeningdocking-validate
- Protein PreparerPDBFixer cleanup, PDB2PQR protonation, and dock-ready structures without MD solvationprotein-prepare
- OpenDDEPredict protein, nucleic acid, and small-molecule complex structures with OpenDDEopendde
- OpenMM MDPrepare, solvate, and equilibrate proteins, small molecules, or membrane systems with OpenMM molecular dynamicsopenmm-md
- MD Trajectory AnalyzerCompute RMSD, Rg, RMSF, ligand H-bond occupancy, and representative frames from OpenMM trajectoriesmd-analyze
- RFAntibodyAntibody and TCR design with RFdiffusion, ProteinMPNN, and RF2 (stages or full pipeline)rfantibody-finetune, rfantibody-pipeline, rfantibody-proteinmpnn, rfantibody-rfdiffusion, rfantibody-tcr-predict
- FreeBindCraftDesign miniprotein and peptide binders against a target structure using open-source scoringfreebindcraft
- GNINAProtein–ligand docking and pose rescoring with convolutional neural network scoring functionsgnina
- Interaction ProfilerEnumerate hydrogen bonds, hydrophobics, salt bridges, and π-stacking in docked complexesplip-profile
- MM-GBSA RescoringEnd-point implicit-solvent MM-GBSA rescoring of docked poses or protein–ligand complexesmm-gbsa
- Relative Binding Free EnergyAlchemical relative binding ΔΔG across ligand perturbation networks, absolute hydration ΔG, and REST2 replica-exchange sampling of protein–ligand complexesopenmm-rbfe
- SurfDockSurface-informed diffusion docking with a reference-ligand pocket and screen-model rescoringsurfdock
- SURFMAP2D projections of protein surface features from PDB structures or SURFMAP matrix filessurfmap
- Thompson SamplingActive-learning virtual screening of un-enumerated combinatorial libraries via Thompson Samplingthompsonsampling
Cheminformatics & Structure
- Fingerprint Similarity & ClusteringTanimoto neighbors, Butina and Leiden clustering, MaxMin diversity picks, and UMAP maps from fingerprintsfingerprint-cluster
- 3D Shape Similarity3D shape and pharmacophore virtual screening against a query conformer with USRCAT and Gaussian overlapshape-similarity
- Image to Structure (OCSR)Read structures and reaction schemes from images of papers and slides as SMILES, checked by a second modelimage-to-structure
- ChEMBL Target ActivitiesPull measured IC50, Ki, Kd, and EC50 values for your targets from ChEMBL into one tablechembl-activities
- Bioactivity Dataset Curator & SplitterNormalize assay units, censoring, and replicates into SAR/QSAR datasets with scaffold, random, or time splitsbioactivity-curate
- Free Wilson AnalysisQuantify R-group SAR contributions and predict unsynthesized molecules from activity datafreewilson
- MolGenGenerate novel, chemically valid analogs of a seed molecule with a SELFIES molecular language modelmolgen
- Matched Molecular PairsHussain–Rea matched pairs: chemical transforms and activity deltas from a SMILES librarymmp-analysis
- Molecule ConversionConvert molecules between SMILES, InChI, SELFIES, MOL/SDF, PDB, and other formats, optionally in 3Dconvert-batch
- Molecule StandardizerSalt-strip, neutralize, tautomer, and stereo cleanup to parent structuresmolecule-standardize
- Reaction EnumerationEnumerate product libraries from reaction SMARTS or RXN files and reactant SMILES listsreaction-enumerate
- Reaction Atom MapperAtom-map reaction SMILES and check element, charge, and stereochemistry balancereaction-map
- Stereoisomer EnumeratorExpand unassigned stereocenters and E/Z double bonds into explicit stereoisomers with a parent-to-isomer auditstereoisomer-enumerate
- Metabolite EnumeratorPredict ranked phase I and phase II metabolite structures with parent and pathway provenancemetabolite-enumerate
- Small-Molecule Force-Field ParameterizerAssign OpenFF Sage force-field parameters and partial charges to small molecules for simulationligand-parameterize
- RMSD CalculatorCalculate the root-mean-square deviation (RMSD) of moleculesmolecule-rmsd-matrix
- PaDEL-DescriptorCompute PaDEL 2D molecular descriptors and fingerprints from SMILES for QSAR and similarity workpadel-descriptor
- RetrosynthesisPropose ranked one-step or short-route retrosynthetic disconnections and building blocks from target SMILESretrosynthesis
- ADMET PredictorPredict 41 ADMET endpoints, including solubility, permeability, CYP, hERG, and toxicity, from SMILESadmet-predict
- Scaffold AnalyzerInventory Bemis–Murcko scaffolds, frequencies, and one representative per scaffold from a SMILES libraryscaffold-analyze
- Structure VisualizerInteractive 3D viewer for proteins, complexes, and small molecules
- Drug-likeness & Structural AlertsScore and filter molecules with Lipinski, Veber, QED, SA score, and PAINS/Brenk/NIH alertsdruglikeness-filter
- Conformer Ensemble GeneratorGenerate an RDKit 3D conformer ensemble per molecule (energy window / RMSD prune)conformer-ensemble
Custom Modeling
- MPNN ModelsFast structure-property inference that highlights key molecule substructuresmodel-score, train-mpnn
- QSAR ModelsCompare random forest, LightGBM, Gaussian process and other QSAR models on your data and keep the besttrain-qsar
- Target RescorerLearn a target-specific score from Vina, GNINA, Boltz-2, MM-GBSA and PLIP signals on your measured compounds, and see which signals predict activitytrain-rescorer
- Active LearningPick the next batch of compounds to make from your measurements, balancing predicted value, uncertainty and diversityactive-learning
- Reaction ModelsPredict reaction yield, selectivity and rates from atom-mapped reactions and their conditionstrain-reaction-mpnn
- Thermo Property ModelsCorrect Joback and Hansen estimates with your own measurements and predict solubility and mixture propertiestrain-thermo-hybrid, train-thermo-mixture
- Python Script SandboxShort RDKit, pandas, NumPy and SciPy analyses of your results, run in isolation with no network accesspython-sandbox
Quantum Chemistry
- PySCF Electronic StructureHartree–Fock, DFT, TDDFT, optimization, frequencies, and charges with PySCF / GPU4PySCFpyscf-electronic
- Qiskit SQDActive-space ground-state energies by sample-based quantum diagonalization on the Qiskit Aer simulatorqiskit-sqd
- xTB / CRESTGFN2-xTB and GFN-FF energies, optimizations, and frequencies, plus CREST conformer and tautomer ensemblesxtb-crest
- Vibrational Spectrum LibraryGFN2-xTB IR spectra for every conformer of an ensemble, plus the Boltzmann-weighted ensemble spectrumvib-spectrum
- PysisyphusGFN-xTB transition states, growing-string and NEB reaction paths, IRCs, and activation barriers between two 3D structurespysisyphus
- QC ThermochemistryZPE, enthalpy, entropy, and Gibbs energy from quantum chemical frequencies with quasi-RRHO corrections, plus NASA-7 polynomials for Canteraqc-thermo
Fluids & Thermodynamics
- CanteraChemical kinetics, thermodynamics, and transport simulations for combustion and reacting flowscantera
- VLE / FlashMulticomponent vapor–liquid phase equilibrium with cubic EOS and UNIFAC or NRTL activity modelsvle-flash
- VLE Thermodynamic Consistency CheckerCheck binary Txy or Pxy vapor–liquid equilibrium data with Gibbs–Duhem area, point, and endpoint testsvle-consistency
- VLE Parameter RegressionFit binary NRTL interaction parameters to measured Txy or Pxy vapor–liquid equilibrium datavle-regress
- Solid–Liquid Equilibrium / Eutectic DiagramBinary liquidus curves, eutectic point, and solubility versus temperature with ideal, NRTL, or UNIFAC activitysle-phase-diagram
- RMG Mechanism GeneratorGenerate Chemkin / Cantera reaction mechanisms with RMG-Py from species, T/P, and terminationrmg-mechanism
- Mechanism ReductionReduce detailed kinetic mechanisms to skeletal Cantera models with DRGEP, DRG, or PFAmechanism-reduce
- Mechanism Target ValidatorBenchmark kinetic mechanisms against measured ignition delays and flame speeds, with per-reaction sensitivity rankingmechanism-validate
- PHREEQC Aqueous SpeciationAqueous speciation, titration, and mixing with USGS PHREEQC for electrolytes and mineral saturationphreeqc
- Group-Contribution PropertiesEstimate Joback and Crippen properties from SMILES for VLE, thermo, and Cantera workflowsgroup-contribution
- Hansen Solubility ParametersEstimate Hansen δD/δP/δH from SMILES and rank solvents by HSP distance, RED, and Flory–Huggins χhansen-hsp
- Kinetic Parameter FitterFit rate constants and Arrhenius parameters to concentration–time data and emit a Cantera YAML mechanismkinetic-fit
- Adsorption Isotherm AnalyzerFit Langmuir, Toth, and Sips isotherms, BET areas, and IAST mixture uptakes to rank porous adsorbentsadsorption-isotherm
- Reaction Calorimetry & Thermal-Safety ModelSimulate batch and semi-batch reaction heat balances and screen thermal-runaway risk with MTSR and TMRadreaction-calorimetry
- NASA / Cantera Species BuilderFit NASA-7 polynomials from a Cp(T) table or Joback properties and emit a Cantera YAML species fragmentnasa-thermo-fit
- Transition-State-Theory Rate CalculatorEyring transition-state-theory rate constants across a temperature range, with fitted Arrhenius parameterstst-rate
- CoolPropOpen CoolProp / IAPWS real-fluid properties: steam tables, refrigerants, and two-phase Helmholtz EOScoolprop