Sometimes it is the simplest scripts that prove to be the most useful. I regularly need to select a specified number of molecules in a
Month: March 2023
Whilst the rule of 5 (Ro5) has provided a useful way to describe small molecule drug space it is also clear that there are a
Much of our understanding of the binding of ligands to kinases has come from crystallographic studies, and there are currently several thousand kinase crystal structures
The RCSB Protein Data Bank is an absolutely invaluable resource that provides archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps scientists
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
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
Workflow tools have become increasingly popular Pipeline Pilot, Knime and Taverna and perhaps the best known. Most are desktop client based but some have a web page that allow users
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.