How to cite TOPO¶

If TOPO contributed to work you are publishing, please cite it. Citing the software lets others find the exact model and version you used, and credits the people who maintain it. If your work is published with the help of TOPO, please also give it a star on GitHub in addition to citing it — it helps others find the project.

Note

No paper or preprint describing TOPO exists yet, so the software entry below is the primary reference. Once a paper is available, cite that as the primary reference and keep the software entry as a secondary, version-specific citation. Keep CITATION.cff at the repository root in sync with this page.

Primary citation¶

Cite the software itself:

Vu, Q. (2026). TOPO: a unified coarse-grained model for globular and disordered proteins (Version 2026.3) [Computer software]. Zenodo. https://doi.org/10.5281/zenodo.21360706

The DOI above is the concept DOI, which always resolves to the latest release.

BibTeX¶

A software entry you can drop into your .bib file:

@software{topo,
  author  = {Vu, Quyen},
  title   = {{TOPO}: a unified coarse-grained model for globular and disordered proteins},
  year    = {2026},
  version = {2026.3},
  doi     = {10.5281/zenodo.21360706},
  url      = {https://github.com/vuqv/topo},
  note     = {Built on OpenMM}
}

Cite the version you used¶

Different TOPO versions can produce different numbers, so record the exact version and, if possible, the commit:

Version — the release tag, or import topo; print(topo.__version__) / the value in pyproject.toml.
Commit — git rev-parse --short HEAD inside the source tree.

If you archive a release on Zenodo (or a similar service), it mints a citable, version-specific DOI. Put the concept DOI (all versions) in the template above and the version DOI in your paper’s methods.

The models TOPO implements¶

TOPO was designed specifically to reproduce the O’Brien-lab coarse-grained and co-translational-synthesis models. After the software itself, these are the most important references to cite — they define the physics TOPO runs. Cite the coarse-grained model whenever you use TOPO at all, and add the CSP reference when you run synthesis (topo-csp / topo-cylinder).

Coarse-grained (structure-based / Gō-like) model¶

The one-bead-per-residue Cα potential — bonds, angles, sequence-dependent dihedrals, and native-contact wells:

O’Brien, E. P., Christodoulou, J., Vendruscolo, M. & Dobson, C. M. Trigger factor slows co-translational folding through kinetic trapping while sterically protecting the nascent chain from aberrant cytosolic interactions. J. Am. Chem. Soc. 134(26):10920–10932 (2012). https://doi.org/10.1021/ja302305u
Jiang, Y. et al. How synonymous mutations alter enzyme structure and function over long timescales. Nat. Chem. 15:308–318 (2023). https://doi.org/10.1038/s41557-022-01091-z

Component potentials of that model, depending on which terms your run uses:

Native-contact wells (LJ 12-10-6). Karanicolas, J. & Brooks III, C. L. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci. 11(10):2351–2361 (2002). https://doi.org/10.1110/ps.0205402
Pairwise contact energies (BT reference-state potential). Betancourt, M. R. & Thirumalai, D. Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci. 8(2):361–369 (1999). https://doi.org/10.1110/ps.8.2.361
Double-well angle potential. Best, R. B., Chen, Y.-G. & Hummer, G. Slow protein conformational dynamics from multiple experimental structures: the helix/sheet transition of arc repressor. Structure 13(12):1755–1763 (2005). https://doi.org/10.1016/j.str.2005.08.009

Co-translational synthesis (CSP) model¶

Used by the topo-csp / topo-cylinder runners. The per-codon, three-stage continuous-synthesis protocol reproduces the O’Brien-lab elongation scheme, described in the same Jiang et al. (2023) paper cited above — cite it here too when you run synthesis.

Other methods and datasets¶

Depending on which parts of the software you use, please also cite the following.

MD engine (always). All dynamics run on OpenMM:

Eastman, P. et al. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. PLoS Comput. Biol. 13(7):e1005659 (2017). https://doi.org/10.1371/journal.pcbi.1005659

Codon dwell-time datasets. If you run synthesis with a species dwell-time table (see Codon dwell-time tables (per-codon timing)), cite the source dataset:

E. coli — Fluitt, A., Pienaar, E. & Viljoen, H. Comput. Biol. Chem. 31:335–346 (2007). https://doi.org/10.1016/j.compbiolchem.2007.07.003
Yeast — Gardin, J. et al. eLife 3:e03735 (2014). https://doi.org/10.7554/eLife.03735
Human — Gobet, C. et al. PNAS 117(17):9630–9641 (2020). https://doi.org/10.1073/pnas.1918145117
N. crassa — Yang, Q. et al. Nucleic Acids Res. 47(17):9243–9258 (2019). https://doi.org/10.1093/nar/gkz710

Machine-readable metadata¶

The repository ships a Citation File Format file, CITATION.cff, at its root. GitHub reads it to show a “Cite this repository” button that exports formatted APA and BibTeX automatically. Keep CITATION.cff and this page in step whenever the citation details change.

Questions¶

For anything not covered here — collaboration, a preprint DOI, or how to cite a specific analysis — open an issue on the GitHub repository.