Welcome to the TOPO documentation

TOPO (TOPOlogy-based coarse-grained model for folded prOteins) is a Python library and command-line toolkit for coarse-grained molecular dynamics of globular (folded) proteins, built on OpenMM. From a single folded-protein structure it builds a one-bead-per-residue, structure-based (Gō-like) model and runs Langevin dynamics — ideal for studying folding, unfolding, thermal/mechanical stability, and multidomain motions.

New here? Read What TOPO does to see the two things TOPO does and jump to the right tutorials, Introduction for installation and package layout, and The TOPO model: theory and force field for what the model is.

Getting started

• What TOPO does
• Interactive diagrams
• Introduction

Tutorials

• TOPO Tutorials
  • Part A — Coarse-grained protein simulation
  • Part B — Translation (protein synthesis)
  • What is TOPO? (the 1-minute version)
  • How you run it
  • Prerequisites
  • Conventions used in the tutorials

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

Indices and tables

• Index

• Module Index

• Search Page