birdday / comp-bio

Databases

Chemical Databases

• PubChemPy: https://pubchempy.readthedocs.io/en/latest/index.html#
• ChemSpyPy: https://chemspipy.readthedocs.io/en/latest/index.html
• ChEMBL: https://www.ebi.ac.uk/chembl/
  • Bioactive molecules with drug-like properties

MOF Databases

• Crystallography Open Database: http://www.crystallography.net/cod/
  • Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.
• Materials Project: https://next-gen.materialsproject.org

Biopolymers

• RCSB PDB: https://www.rcsb.org
  • Royal Chemical Society PDB
• wwPDB: https://www.wwpdb.org
  • Worldwide Protein Data Bank

Misc.

• CCDC: https://www.ccdc.cam.ac.uk/structures/Search?Ccdcid=Ibuprofen&DatabaseToSearch=Published
  • Cambridge Crystallographic Structure Database

List of Databases

• https://www-library.ch.cam.ac.uk/list-useful-databases
• https://mof-international.org/mof-structures/

Comp. Chem. Python Packages

Documentation

• RDKIT: https://www.rdkit.org/docs/
• ASE: https://wiki.fysik.dtu.dk/ase/

Tutorials

• https://www.insilicochemistry.io/tutorials/foundations/intro-to-cheminformatics-with-rdkit

List of Packages

• https://github.com/lmmentel/awesome-python-chemistry