I’ve recently become interested the comparison of the amino amino-acid composition of peptides, to allow comparison of cyclic versus linear peptides, or brain penetrant verses
Author: chris
Sometimes I have two datasets and I just want to know the overlap of identical structures. This script counts the number of identical structures by
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
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