Tools
76 tools, one method at a time.
Every model and method behind the workflows, plus quantum chemistry, thermodynamics, and custom models. Each page lists the hardware it runs on, the price per run on each plan, its inputs and outputs, and the papers behind it.
Solving a whole problem rather than running one method? Start from a ready-made workflow
76 tools
- DiffDockProtein-ligand docking with diffusion models and confidence-ranked poses
- DrugFlowGenerate candidate ligands from a protein target and reference ligand using flow matching
- Sequence MutatorApply point mutations such as T315I to a protein sequence, checking each wild-type residue
- ESMFold2Predict protein, DNA, RNA, and ligand complex structures with evolutionary scale modeling
- Evo 2Genome modeling and design across all domains of life with the Evo 2 DNA language model
- AutoDock VinaHigh performance molecular docking and virtual screening for drug discovery
- Binding-Site DetectorFind ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflows
- Docking Protocol ValidatorRedock co-crystallized ligands and score pose RMSD and enrichment to validate a docking setup before screening
- Protein PreparerPDBFixer cleanup, PDB2PQR protonation, and dock-ready structures without MD solvation
- OpenDDEPredict protein, nucleic acid, and small-molecule complex structures with OpenDDE
- OpenMM MDPrepare, solvate, and equilibrate proteins, small molecules, or membrane systems with OpenMM molecular dynamics
- MD Trajectory AnalyzerCompute RMSD, Rg, RMSF, ligand H-bond occupancy, and representative frames from OpenMM trajectories
- RFAntibodyAntibody and TCR design with RFdiffusion, ProteinMPNN, and RF2 (stages or full pipeline)
- FreeBindCraftDesign miniprotein and peptide binders against a target structure using open-source scoring
- GNINAProtein–ligand docking and pose rescoring with convolutional neural network scoring functions
- Interaction ProfilerEnumerate hydrogen bonds, hydrophobics, salt bridges, and π-stacking in docked complexes
- MM-GBSA RescoringEnd-point implicit-solvent MM-GBSA rescoring of docked poses or protein–ligand complexes
- Relative Binding Free EnergyAlchemical relative binding ΔΔG across ligand perturbation networks, absolute hydration ΔG, and REST2 replica-exchange sampling of protein–ligand complexes
- SurfDockSurface-informed diffusion docking with a reference-ligand pocket and screen-model rescoring
- SURFMAP2D projections of protein surface features from PDB structures or SURFMAP matrix files
- MPNN ModelsFast structure-property inference that highlights key molecule substructures
- QSAR ModelsCompare random forest, LightGBM, Gaussian process and other QSAR models on your data and keep the best
- 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 activity
- Active LearningPick the next batch of compounds to make from your measurements, balancing predicted value, uncertainty and diversity
- Reaction ModelsPredict reaction yield, selectivity and rates from atom-mapped reactions and their conditions
- Thermo Property ModelsCorrect Joback and Hansen estimates with your own measurements and predict solubility and mixture properties
- Python Script SandboxShort RDKit, pandas, NumPy and SciPy analyses of your results, run in isolation with no network access
- Thompson SamplingActive-learning virtual screening of un-enumerated combinatorial libraries via Thompson Sampling
- Fingerprint Similarity & ClusteringTanimoto neighbors, Butina and Leiden clustering, MaxMin diversity picks, and UMAP maps from fingerprints
- 3D Shape Similarity3D shape and pharmacophore virtual screening against a query conformer with USRCAT and Gaussian overlap
- Image to Structure (OCSR)Read structures and reaction schemes from images of papers and slides as SMILES, checked by a second model
- ChEMBL Target ActivitiesPull measured IC50, Ki, Kd, and EC50 values for your targets from ChEMBL into one table
- Bioactivity Dataset Curator & SplitterNormalize assay units, censoring, and replicates into SAR/QSAR datasets with scaffold, random, or time splits
- Free Wilson AnalysisQuantify R-group SAR contributions and predict unsynthesized molecules from activity data
- MolGenGenerate novel, chemically valid analogs of a seed molecule with a SELFIES molecular language model
- Matched Molecular PairsHussain–Rea matched pairs: chemical transforms and activity deltas from a SMILES library
- Molecule ConversionConvert molecules between SMILES, InChI, SELFIES, MOL/SDF, PDB, and other formats, optionally in 3D
- Molecule StandardizerSalt-strip, neutralize, tautomer, and stereo cleanup to parent structures
- Reaction EnumerationEnumerate product libraries from reaction SMARTS or RXN files and reactant SMILES lists
- Reaction Atom MapperAtom-map reaction SMILES and check element, charge, and stereochemistry balance
- Stereoisomer EnumeratorExpand unassigned stereocenters and E/Z double bonds into explicit stereoisomers with a parent-to-isomer audit
- Metabolite EnumeratorPredict ranked phase I and phase II metabolite structures with parent and pathway provenance
- Small-Molecule Force-Field ParameterizerAssign OpenFF Sage force-field parameters and partial charges to small molecules for simulation
- RMSD CalculatorCalculate the root-mean-square deviation (RMSD) of molecules
- PaDEL-DescriptorCompute PaDEL 2D molecular descriptors and fingerprints from SMILES for QSAR and similarity work
- RetrosynthesisPropose ranked one-step or short-route retrosynthetic disconnections and building blocks from target SMILES
- ADMET PredictorPredict 41 ADMET endpoints, including solubility, permeability, CYP, hERG, and toxicity, from SMILES
- Scaffold AnalyzerInventory Bemis–Murcko scaffolds, frequencies, and one representative per scaffold from a SMILES library
- Structure VisualizerInteractive 3D viewer for proteins, complexes, and small molecules
- CanteraChemical kinetics, thermodynamics, and transport simulations for combustion and reacting flows
- VLE / FlashMulticomponent vapor–liquid phase equilibrium with cubic EOS and UNIFAC or NRTL activity models
- VLE Thermodynamic Consistency CheckerCheck binary Txy or Pxy vapor–liquid equilibrium data with Gibbs–Duhem area, point, and endpoint tests
- VLE Parameter RegressionFit binary NRTL interaction parameters to measured Txy or Pxy vapor–liquid equilibrium data
- Solid–Liquid Equilibrium / Eutectic DiagramBinary liquidus curves, eutectic point, and solubility versus temperature with ideal, NRTL, or UNIFAC activity
- RMG Mechanism GeneratorGenerate Chemkin / Cantera reaction mechanisms with RMG-Py from species, T/P, and termination
- Mechanism ReductionReduce detailed kinetic mechanisms to skeletal Cantera models with DRGEP, DRG, or PFA
- Mechanism Target ValidatorBenchmark kinetic mechanisms against measured ignition delays and flame speeds, with per-reaction sensitivity ranking
- PHREEQC Aqueous SpeciationAqueous speciation, titration, and mixing with USGS PHREEQC for electrolytes and mineral saturation
- Group-Contribution PropertiesEstimate Joback and Crippen properties from SMILES for VLE, thermo, and Cantera workflows
- Hansen Solubility ParametersEstimate Hansen δD/δP/δH from SMILES and rank solvents by HSP distance, RED, and Flory–Huggins χ
- Kinetic Parameter FitterFit rate constants and Arrhenius parameters to concentration–time data and emit a Cantera YAML mechanism
- Adsorption Isotherm AnalyzerFit Langmuir, Toth, and Sips isotherms, BET areas, and IAST mixture uptakes to rank porous adsorbents
- Reaction Calorimetry & Thermal-Safety ModelSimulate batch and semi-batch reaction heat balances and screen thermal-runaway risk with MTSR and TMRad
- NASA / Cantera Species BuilderFit NASA-7 polynomials from a Cp(T) table or Joback properties and emit a Cantera YAML species fragment
- Transition-State-Theory Rate CalculatorEyring transition-state-theory rate constants across a temperature range, with fitted Arrhenius parameters
- Drug-likeness & Structural AlertsScore and filter molecules with Lipinski, Veber, QED, SA score, and PAINS/Brenk/NIH alerts
- CoolPropOpen CoolProp / IAPWS real-fluid properties: steam tables, refrigerants, and two-phase Helmholtz EOS
- Conformer Ensemble GeneratorGenerate an RDKit 3D conformer ensemble per molecule (energy window / RMSD prune)
- PySCF Electronic StructureHartree–Fock, DFT, TDDFT, optimization, frequencies, and charges with PySCF / GPU4PySCF
- Qiskit SQDActive-space ground-state energies by sample-based quantum diagonalization on the Qiskit Aer simulator
- xTB / CRESTGFN2-xTB and GFN-FF energies, optimizations, and frequencies, plus CREST conformer and tautomer ensembles
- Vibrational Spectrum LibraryGFN2-xTB IR spectra for every conformer of an ensemble, plus the Boltzmann-weighted ensemble spectrum
- PysisyphusGFN-xTB transition states, growing-string and NEB reaction paths, IRCs, and activation barriers between two 3D structures
- QC ThermochemistryZPE, enthalpy, entropy, and Gibbs energy from quantum chemical frequencies with quasi-RRHO corrections, plus NASA-7 polynomials for Cantera