Ready-made workflows that chain several tools into one run.
88 tools
3D shape and pharmacophore virtual screening against a query conformer with USRCAT and Gaussian overlap
Pick the next batch of compounds to make from your measurements, balancing predicted value, uncertainty and diversity
Predict 41 ADMET endpoints, including solubility, permeability, CYP, hERG, and toxicity, from SMILES
Fit Langmuir, Toth, and Sips isotherms, BET areas, and IAST mixture uptakes to rank porous adsorbents
Number antibody, nanobody and TCR variable domains (IMGT, Kabat, Chothia), mark CDRs and assign the nearest human germline
Rank antibody variants by predicted change in binding free energy on an antibody-antigen complex
Find ligandable pockets and emit Vina-shaped docking boxes for fold-to-dock workflows
Normalize assay units, censoring, and replicates into SAR/QSAR datasets with scaffold, random, or time splits
Pull measured IC50, Ki, Kd, and EC50 values for your targets from ChEMBL into one table
Generate an RDKit 3D conformer ensemble per molecule (energy window / RMSD prune)
Redock co-crystallized ligands and score pose RMSD and enrichment to validate a docking setup before screening
Fit raw dose-response readings to 4PL, 5PL, or Morrison models with replicate QC for IC50, EC50, and Ki values ready for curation
Score and filter molecules with Lipinski, Veber, QED, SA score, and PAINS/Brenk/NIH alerts
Tanimoto neighbors, Butina and Leiden clustering, MaxMin diversity picks, and UMAP maps from fingerprints
Quantify R-group SAR contributions and predict unsynthesized molecules from activity data
Design miniprotein and peptide binders against a target structure using open-source scoring
Estimate Joback and Crippen properties from SMILES for VLE, thermo, and Cantera workflows
Estimate Hansen δD/δP/δH from SMILES and rank solvents by HSP distance, RED, and Flory–Huggins χ
Read structures and reaction schemes from images of papers and slides as SMILES, checked by a second model
Enumerate hydrogen bonds, hydrophobics, salt bridges, and π-stacking in docked complexes
Fit rate constants and Arrhenius parameters to concentration–time data and emit a Cantera YAML mechanism
Hussain–Rea matched pairs: chemical transforms and activity deltas from a SMILES library
Compute RMSD, Rg, RMSF, ligand H-bond occupancy, and representative frames from OpenMM trajectories
Reduce detailed kinetic mechanisms to skeletal Cantera models with DRGEP, DRG, or PFA
Benchmark kinetic mechanisms against measured ignition delays and flame speeds, with per-reaction sensitivity ranking
Predict ranked phase I and phase II metabolite structures with parent and pathway provenance
End-point implicit-solvent MM-GBSA rescoring of docked poses or protein–ligand complexes
Convert molecules between SMILES, InChI, SELFIES, MOL/SDF, PDB, and other formats, optionally in 3D
Salt-strip, neutralize, tautomer, and stereo cleanup to parent structures
Design amino-acid sequences for a fixed protein backbone with ProteinMPNN, LigandMPNN or SolubleMPNN
Fit NASA-7 polynomials from a Cp(T) table or Joback properties and emit a Cantera YAML species fragment
Compute PaDEL 2D molecular descriptors and fingerprints from SMILES for QSAR and similarity work
Aqueous speciation, titration, and mixing with USGS PHREEQC for electrolytes and mineral saturation
Screen protein and antibody chains for pI, charge, GRAVY, instability, and sequence liability motifs
PDBFixer cleanup, PDB2PQR protonation, and dock-ready structures without MD solvation
Compare predicted or designed protein structures by TM-score and RMSD, cluster them, and pick one representative per fold
Hartree–Fock, DFT, TDDFT, optimization, frequencies, and charges with PySCF / GPU4PySCF
GFN-xTB transition states, growing-string and NEB reaction paths, IRCs, and activation barriers between two 3D structures
Short RDKit, pandas, NumPy and SciPy analyses of your results, run in isolation with no network access
ZPE, enthalpy, entropy, and Gibbs energy from quantum chemical frequencies with quasi-RRHO corrections, plus NASA-7 polynomials for Cantera
Active-space ground-state energies by sample-based quantum diagonalization on the Qiskit Aer simulator
Compare random forest, LightGBM, Gaussian process and other QSAR models on your data and keep the best
Atom-map reaction SMILES and check element, charge, and stereochemistry balance
Simulate batch and semi-batch reaction heat balances and screen thermal-runaway risk with MTSR and TMRad
Enumerate product libraries from reaction SMARTS or RXN files and reactant SMILES lists
Predict reaction yield, selectivity and rates from atom-mapped reactions and their conditions
Alchemical relative binding ΔΔG across ligand perturbation networks, absolute hydration ΔG, and REST2 replica-exchange sampling of protein–ligand complexes
Propose ranked one-step or short-route retrosynthetic disconnections and building blocks from target SMILES
Antibody and TCR design with RFdiffusion, ProteinMPNN, and RF2 (stages or full pipeline)
Generate all-atom protein backbones under motif, ligand, binder and symmetry constraints
Design protein, RNA and DNA backbones, and protein-nucleic-acid complexes, under motif, ligand and symmetry constraints
Improve a protein binder design by cycling RoseTTAFold3 or Boltz-2 prediction with LigandMPNN redesign
Generate Chemkin / Cantera reaction mechanisms with RMG-Py from species, T/P, and termination
Predict the structure of protein, DNA, RNA and ligand complexes with all-atom RoseTTAFold3 and an independent confidence score
Inventory Bemis–Murcko scaffolds, frequencies, and one representative per scaffold from a SMILES library
Apply point mutations such as T315I to a protein sequence, checking each wild-type residue
Assign OpenFF Sage force-field parameters and partial charges to small molecules for simulation
Binary liquidus curves, eutectic point, and solubility versus temperature with ideal, NRTL, or UNIFAC activity
Expand unassigned stereocenters and E/Z double bonds into explicit stereoisomers with a parent-to-isomer audit
Grade protein model geometry: Ramachandran and rotamer outliers, atomic clashes, cis-peptides, C-beta deviation and ligand bond geometry
Learn a target-specific score from Vina, GNINA, Boltz-2, MM-GBSA and PLIP signals on your measured compounds, and see which signals predict activity
Correct Joback and Hansen estimates with your own measurements and predict solubility and mixture properties
Active-learning virtual screening of un-enumerated combinatorial libraries via Thompson Sampling
Eyring transition-state-theory rate constants across a temperature range, with fitted Arrhenius parameters
GFN2-xTB IR spectra for every conformer of an ensemble, plus the Boltzmann-weighted ensemble spectrum
Multicomponent vapor–liquid phase equilibrium with cubic EOS and UNIFAC or NRTL activity models
Fit binary NRTL interaction parameters to measured Txy or Pxy vapor–liquid equilibrium data
Check binary Txy or Pxy vapor–liquid equilibrium data with Gibbs–Duhem area, point, and endpoint tests
GFN2-xTB and GFN-FF energies, optimizations, and frequencies, plus CREST conformer and tautomer ensembles