In the previous workflow I described docking a set of ligands with known activity into a target protein, in this workflow we will be using a set
Year: 2023
Whilst high-throughput screening (HTS) has been the starting point for many successful drug discovery programs the cost of screening, the lack of accessibility of a
A little while back I described a docking workflow including a rescoring script for Vortex, so I thought it might be useful to include this on a
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
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