The PDB api has been changed so these scripts no longer work, updated scripts can be found here https://macinchem.org/2025/04/05/two-vortex-scripts-for-interacting-with-pdb/ The RCSB Protein Data Bank is an absolutely
Tag: cheminformatics
It is really useful to have two sites of metabolism tools available that use contrasting methodologies, FAME 2 using curated dataset of experimentally determined metabolism
A while back I published two scripts that use UniChem a web resource provided by the EBI, a ‘Unified Chemical Identifier’ system, designed to assist in the
I recently wrote a review of Reaction Workflows, a web-based tool that allow users to build workflows from nodes that provide inputs and outputs or perform
Too often I come across datasets that Chemical names or identifiers but no actual molecular structure, recently Dan at Dotmatics suggested I look at OPSIN.
I often need to tag individual molecules within a dataset with a specific property, perhaps the results of clustering algorithms, the results of PAINS filtering, or Liver
ZINC is a free database of commercially-available compounds for virtual screening. ZINC contains over 100 million purchasable compounds in ready-to-dock, 3D formats. Sterling and Irwin, J. Chem.
Just a quick tip. Sometimes I have a column in a Vortex workspace that I want to access via script where the title is something
UniChem is a web resource provided by the EBI, it is a ‘Unified Chemical Identifier’ system, designed to assist in the rapid cross-referencing of chemical structures,
UniChem is a web resource provided by the EBI, it is a ‘Unified Chemical Identifier’ system, designed to assist in the rapid cross-referencing of chemical structures,