CogniChem Application

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

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Modeling and analysis tools for biomolecular research

AutoDock VinaHigh performance molecular docking and virtual screening for drug discovery

Boltz-2Accurate in silico screening for early-stage drug discovery

BoltzGenDesign proteins and peptides to bind biomolecular targets

DiffDockProtein-ligand docking with diffusion models and confidence-ranked poses

DrugFlowGenerate candidate ligands from a protein target and reference ligand using flow matching

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

FreeBindCraftDesign miniprotein and peptide binders against a target structure using open-source scoring

GNINACNN-accelerated protein–ligand docking and rescoring

OpenDDEPredict protein, nucleic acid, and small-molecule complex structures with OpenDDE

OpenMM MDPrepare, solvate, and equilibrate protein structures with OpenMM molecular dynamics

RFAntibodyAntibody and TCR design with RFdiffusion, ProteinMPNN, and RF2 (stages or full pipeline)

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

Thompson SamplingActive-learning virtual screening of un-enumerated combinatorial libraries via Thompson Sampling

General-purpose tools for working with molecular structures and data

Conformer 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 alerts

Fingerprint Similarity & ClusteringTanimoto nearest neighbors, Butina clustering, MaxMin diversity, and Scanpy PCA/UMAP/Leiden clustering from molecular fingerprints

Free Wilson AnalysisQuantify R-group SAR contributions and predict unsynthesized molecules from activity data

Matched Molecular PairsHussain–Rea matched pairs: chemical transforms and activity deltas from a SMILES library

Molecule ConversionConvert molecule file/data format

Molecule StandardizerSalt-strip, neutralize, tautomer, and stereo cleanup to parent structures

PaDEL-DescriptorCalculate molecular descriptors and fingerprints

Reaction EnumerationEnumerate product libraries from reaction SMARTS or RXN files and reactant SMILES lists

RetrosynthesisPropose ranked one-step or short-route retrosynthetic disconnections and building blocks from target SMILES

RMSD CalculatorCalculate the root-mean-square deviation (RMSD) of molecules

Structure VisualizerInteractive 3D viewer for proteins, complexes, and small molecules

Chemical kinetics, phase equilibrium, thermodynamics, and transport simulations

CanteraChemical kinetics, thermodynamics, and transport simulations for combustion and reacting flows

CoolPropOpen CoolProp / IAPWS real-fluid properties: steam tables, refrigerants, and two-phase Helmholtz EOS

Group-Contribution PropertiesEstimate Joback and Crippen properties from SMILES for VLE, thermo, and Cantera workflows

PHREEQC Aqueous SpeciationAqueous speciation, titration, and mixing with USGS PHREEQC for electrolytes and mineral saturation

RMG Mechanism GeneratorGenerate Chemkin / Cantera reaction mechanisms with RMG-Py from species, T/P, and termination

VLE / FlashMulticomponent vapor–liquid phase equilibrium with cubic EOS and UNIFAC or NRTL activity models

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

MPNN ModelsFast structure-property inference that highlights key molecule substructures