Protein–protein complex — on hold

On hold since 2026-10-13

MD-tools is now dedicated to sampling the conformations of a ligand, in solvent or in a protein. A protein–protein complex, where the quantity of interest is the association of two folded chains, is outside that. Nothing here is part of the current release, and the tutorial was last run against 0.6.1. See On hold for what else is waiting.

What exists

part	what it is	last run against
Barnase and barstar	the system: PDB 1BRS, biological assembly 3, built in explicit water	0.6.1
cMD: barnase–barstar	10 ns of production from the deposited crystal structure, with the analysis script	0.6.1

What stays in MD-tools

The code that builds and runs a protein complex is not removed: a protein is still built from a .pdb, protonated by PROPKA, solvated and run. What is on hold is the topic: tutorials, planned pages and release testing for protein–protein association. A protein carrying a ligand is the supported case, and is not on hold.

What would take it off hold

A decision that protein–protein sampling is back in scope, and the tutorial re-run on the then-current release, because every number on it was produced by 0.6.1.