Research Blog

We've all seen it in results sections: "RMSD = 1.8". But that single number hides several assumptions worth stating explicitly. 1. Units. Most tools report in Ångströms, but not all — GROMACS, for instance, outputs in nanometres. If you don't specify, "1.8" is ambiguous. State the unit. 2. Which atoms? When superposing protein structures, RMSD changes with the atom set: Cα only, backbone (N, Cα, C), main chain (N, Cα, C, O), or all atoms. The same two structures give very dif

Figure was adapted from ColabFold presentation Why might AlphaFold & Co. struggle predicting complexes for non-host-beneficial proteins? I work on transposons - mobile DNA elements that encode proteins capable of cutting and pasting their own sequence within a genome. Fascinating biology, but also quite “selfish” and potentially harmful to the host. I have noticed that AlphaFold Multimer often struggles to predict protein–protein or protein-DNA complexes for these systems. On

Like coffee and chromatography? Fun fact: brewing a perfect espresso is a lot like doing chromatography with broken fraction collector, where you only have one tube to collect extract. Good espresso requires some tuning, but let’s simplify for clarity. For a double espresso, take 14 g of ground coffee and extract it with a 1:2 brew ratio – that is, 28 g of water – over 30 seconds. This corresponds to a flow rate of roughly 60 mL/min. Assuming a homogeneous distribution of cof