CogniChem Application

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

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

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

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

Molecule ConversionConvert molecule file/data format

PaDEL-DescriptorCalculate molecular descriptors and fingerprints

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

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

Chemical kinetics, thermodynamics, and transport simulations

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

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

MPNN ModelsFast structure-property inference that highlights key molecule substructures