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TOPO rc1 documentation
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TOPO rc1 documentation

Getting started

  • What TOPO does
  • Interactive diagrams
  • Introduction

Tutorials

  • TOPO Tutorials
    • Tutorial 1 — Single-domain quickstart
    • Tutorial 2 — Multidomain proteins & per-domain contact scaling
    • Tutorial 3 — Restarting a run & understanding the outputs
    • Tutorial 4 — Many copies in one run (better GPU utilization)
    • Tutorial 5 — Optimizing the contact nscale (nscale)
    • Tutorial 6 — Temperature annealing & quenching
    • Tutorial 7 — Protein synthesis through an analytic exit tunnel
    • Tutorial 8 — Protein synthesis on a coarse-grained ribosome

The TOPO model

  • The TOPO model: theory and force field

Isolated-protein simulations

  • Simulation control options
  • Domain definition file (domain.yaml)
  • Native-contact analysis (the Q score)
  • Output files and the run log

Protein synthesis

  • Protein synthesis: overview
  • The ribosome structure (get one, or build your own)
  • Codon dwell-time tables (per-codon timing)
  • Synthesis in coarse-grained ribosome model
  • Synthesis in cylinder ribosome model
  • Synthesis control options

Python & API reference

  • Using TOPO from Python
  • Parameters
  • System
  • Models
  • topo.reporter package

Full module index

  • topo
    • topo package
      • topo.analysis package
      • topo.core package
      • topo.csp package
      • topo.mdrun package
      • topo.optimize package
      • topo.utils package
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