Tagged chemistry

Enumerate virtual compound libraries from building blocks with reaction SMARTS

Extract and deduplicate reads by UMI to count molecules accurately with umi_tools

Find structural analogs by Tanimoto similarity and cluster compounds with Butina

Find compounds that contain a substructure using SMARTS patterns in RDKit

Dock compound libraries into a protein site with AutoDock Vina and rank them

Analyze living systems through evolution, molecular biology and ecology lenses

Search the ChEMBL bioactive molecules database with plain language queries

Analyze reactions, synthesis and spectroscopy data through a chemistry lens

Handle SMILES, descriptors, fingerprints and conformers with a simple RDKit wrapper

Train molecular machine learning models for ADMET and toxicity with DeepChem

Find small molecule binders for a protein target with docking and ADMET profiles

Retrieve compound identifiers, properties and bioactivity from PubChem and ChEMBL

Predict chemical toxicity for AMES, DILI and LD50 with safety label data

Predict molecular ADMET properties and generate molecules with graph neural networks

Route chemistry research questions to the right chemistry skill and data workflow

Compute molecular descriptors, fingerprints and feature quality checks for compounds

Clean and audit structured chemical reaction records for duplicates and mass balance

Resolve chemical names and identifiers like SMILES, InChIKey and CAS numbers

Search and curate compound libraries by similarity, substructure and diversity

Find and compare past chemical reactions by ID, components, SMARTS or similarity

Batch-standardize chemical structures from SMILES, SDF and CSV files, removing salts

Dock small molecules into protein pockets with DiffDock-L blind diffusion docking

Control Hayward OmniLogic pool equipment, chemistry logs and schedules

Set up and run LAMMPS molecular dynamics simulations with the DeePMD-kit plugin

Query ChEMBL for bioactive molecules, targets, bioactivities and approved drugs

Sort lab chemicals into safe storage groups and flag incompatible pairs

Convert chemical names, SMILES and molecular formulas and validate structures

Query CTD for chemical, gene, disease and pathway interactions in toxicogenomics

Write photorealistic molecule rendering scripts for PyMOL and ChimeraX

Parse and standardize SMILES and compute descriptors and fingerprints with datamol

Predict blind ligand-protein binding poses with DiffDock and confidence scores

Map disease mechanisms from molecules and pathways to clinical phenotypes

Write a PubMed-based review of a molecule in disease with Vancouver citations

Plan network toxicology and molecular docking studies for a toxicant and disease

Run cloud quantum chemistry jobs for pKa, geometry optimization and docking from Python

Extract hazard codes and safety data from chemical safety datasheets

Plan network toxicology studies linking one compound to one disease with docking

Remove salt counterions from SMILES structures and standardize molecules

Match patient profiles to ranked ClinicalTrials.gov trials by molecular eligibility

Build graph neural networks for molecules and proteins in PyTorch

Find the right colored waste container for each lab chemical with safety notes

Look up purchasable ZINC compounds by ID or SMILES and download docking-ready structures

Map chemicals to adverse outcome pathways from molecular event to organ toxicity

Find small-molecule binders for protein targets through virtual screening and filtering

Look up compound names as SMILES, InChI and CIDs from PubChem and ChEMBL

Assess chemical hazards and toxicity using CTD, GHS and IARC data

Find chemical vendors and in-stock analogs in ZINC, Enamine and eMolecules

Match patient molecular profiles to ranked oncology clinical trials

Work out crystal lattice, coordination geometry and thermodynamic properties