Tagged chemistry

Identify whether a compound is a known natural product and classify its chemistry

Predict organic reaction products and interpret NMR, IR and mass spectra

Recommend cancer therapies and trials from a tumor molecular profile

Trace compound names to activity, ADMET and purchasable stock with PubChem and ChEMBL

Assess drug and chemical toxicity from adverse outcome pathways and FAERS signals

Animate chemical reactions in 3D with balanced equations and atom counts

Make chemistry explainer videos from problem screenshots with voice-over and subtitles

Decompose exposure effects into direct and mediated paths for molecular mediators

Generate 3D conformer ensembles with RDKit ETKDG and force-field refinement

Delimit species from molecular data with ASAP, mPTP and GMYC

Design novel molecules with REINVENT and diffusion models for multi-goal optimization

Predict peptide binding to MHC class II molecules for CD4 epitope discovery

Track ctDNA across serial blood draws for molecular residual disease monitoring

Predict and rescore protein-ligand poses with DiffDock, Boltz and Chai

Compute molecular fingerprints and physicochemical descriptors with RDKit

Read and convert SMILES, SDF, MOL2 and PDB molecule files with RDKit and Open Babel

Standardize chemical structures with the ChEMBL pipeline and RDKit tautomer rules

Estimate divergence times with molecular clocks, calibrations and BEAST2

Design PROTACs and molecular glues with ligase choice, linkers and ternary models

Enumerate virtual compound libraries from reaction SMARTS with RDKit

Collapse UMI reads to molecules with umi_tools and fgbio consensus calling

Calculate GC skew, melting temperature, molecular weight and pI for sequences

Find similar molecules with Tanimoto, Tversky and Dice on fingerprints

Analyze alternative splicing in single cells and pick the right library chemistry

Prepare protein structures for docking and MD with hydrogens and protonation

Run structure-based virtual screening with Vina, GNINA and DiffDock

Prepare, run and check LAMMPS molecular dynamics and stress-strain studies

Compute GC, ORFs, molecular weight and other metrics for a FASTA sequence file

Run nf-core RNA structure analysis from chemical probing reads to 2D diagrams

Parse molecules, compute descriptors and run substructure searches with RDKit

Balance reactions, run thermodynamics and query PubChem for molecular data

Run molecular dynamics with OpenMM and analyze trajectories and binding

Analyze protein 3D structures, homology models, AlphaFold output and docking

Build crystal structures, phase diagrams and VASP input with pymatgen

Work with SMILES, molecular properties and fingerprints using RDKit

Predict HIV inhibition and other molecular activity from SMILES strings