Welcome to the TOPO documentation¶
TOPO is a unified coarse-grained model for globular and disordered proteins, built on OpenMM — a Python library and command-line toolkit. From a single structure it builds a one-bead-per-residue, structure-based (Gō-like) model and runs Langevin dynamics, for studying folding, unfolding, thermal/mechanical stability, and multidomain motions. Unified means one force field spans the whole spectrum: globular (folded) proteins, multi-domain proteins with intrinsically disordered regions, and fully disordered proteins (IDPs) — see Disordered / IDR regions.
New here? Read What TOPO does to see the two things TOPO does and jump to the right tutorials, How to install to get it running, Introduction for the package layout, and The TOPO model: theory and force field for what the model is.
Lineage. TOPO implements the models developed in the O’Brien lab (E. P. O’Brien and co-workers): the coarse-grained structure-based model of O’Brien et al. (2012) and the per-codon co-translational-synthesis (CSP) protocol of Jiang et al. (2023). Its physics and elongation kinetics reproduce that work. If you publish with TOPO, please cite those references alongside the software — see How to cite TOPO for the full list with DOIs.
Getting started
Tutorials
The TOPO model
Domain stability optimization
Isolated-protein simulations
Protein synthesis
Python & API reference
Full module index