Codon dwell-time tables (per-codon timing)

Per-codon timing (Synthesis in coarse-grained ribosome model) needs a codon dwell-time table — the codon_times key of a csp.ini / cylinder.ini. It maps each codon to its mean in-vivo per-codon translation (dwell) time in seconds (the codon’s mean first-passage time), which is what sets each residue’s MD-segment length. There is no bundled default: you pick a table for your organism (and, where relevant, elongation rate). TOPO ships a small library of them.

Where they live & the format

The tables are under assets/csp/codon_dwell_times/<organism>/. Each is a plain text file, one row per codon:

# codon   dwell_time_seconds   amino_acid
UUU       0.068164             PHE
...
UAA       0.005513             STOP

  • RNA alphabet (U), tab-separated, # comments ignored; 64 rows (61 sense + 3 stop). Larger time = slower codon; stop codons carry the amino acid STOP.

  • The third column (amino acid) is what mrna = fastest/slowest/median uses to pick each residue’s synonymous codon — see Fastest / slowest / median mRNA.

  • Every organism directory also has a *_dwell_time_methods.md with the full provenance (source dataset, references, how relative data were scaled to seconds).

Shipped tables

Organism

File(s)

Basis (see the methods note for full provenance)

E. coli

ecoli_codon_dwell_times_310K.txt

Fluitt, Pienaar & Viljoen (2007) mechanistic decoding times, O’Brien-rescaled so the codon-usage-weighted mean = 0.061 s/codon (16.5 aa/s) at 310 K. Absolute; the most-validated table.

S. cerevisiae

yeast_codon_dwell_times.txt

Gardin et al. (2014) relative decoding rates (RRT), frequency-weighted → seconds (~0.108 s/codon; ~9.3 codons/s).

yeast_codon_dwell_times_OBrien.txt

O’Brien-lab chemical-kinetic model, absolute (~0.233 s/codon; ~4.3 codons/s) — the most pipeline-native yeast table.

yeast_codon_dwell_times_OBrien_rescaled_9.3.txt

The O’Brien table rescaled to 9.3 aa/s (matches the Gardin rate).

H. sapiens

human_codon_dwell_times.txt

Gobet et al. (2020) liver ribosome-profiling dwell times (Lintner dataset) → seconds.

human_codon_dwell_times_v2_freqweighted.txt

Same, frequency-weighted to an elongation-rate anchor R = 5.6 codons/s.

N. crassa

ncrassa_codon_dwell_times_R{5.35_low,6.7_mid,8.02_high}.txt

Yang et al. (2019) relative codon decoding times (RCDT) → seconds at three measured elongation-rate anchors (5.35 / 6.7 / 8.02 codons/s). Least-certain table (relative values digitized from a figure).

..._v2_freqweighted.txt (× 3)

Frequency-weighted variants of the three anchors.

Frequency-weighted (v2) variants. These rescale the per-codon times so the codon-usage-weighted mean over the organism’s transcriptome hits the target elongation rate, instead of an unweighted mean. Use them when you want the genome-wide average speed to match the anchor; use the plain (v1) tables for the raw per-codon values.

Note

References — E. coli: Fluitt, Pienaar & Viljoen, Comput. Biol. Chem. 31:335–346 (2007). Yeast: Gardin et al., eLife 3:e03735 (2014). Human: Gobet et al., PNAS 117(17):9630–9641 (2020). N. crassa: Yang et al., Nucleic Acids Res. 47(17):9243–9258 (2019).

Use one in a run

Point the codon_times key at a table (a path selects per-codon timing; a plain number would instead mean a uniform time for every codon):

pdb_file    = my_protein.pdb
mrna        = my_protein_mrna.txt
codon_times = assets/csp/codon_dwell_times/ecoli/ecoli_codon_dwell_times_310K.txt

Keep the thermostat consistent with the table’s temperature: ref_t defaults to 310 K to match the E. coli table — set it to your table’s temperature if it differs. See Synthesis control options for the full key reference.

Fastest / slowest / median mRNA

Because each table carries the codon→amino-acid mapping (column 3), you can set mrna = fastest, slowest or median (instead of a sequence file) to auto-build a synonymous-codon mRNA that encodes your protein with every residue’s fastest/slowest/ median-dwell-time codon for the chosen table — the extremes of the codon-optimization axis, or a neutral middle reference. See Fastest / slowest / median (synonymous-codon) mRNA, or pre-generate one standalone:

topo-make-mrna --pdb my_protein.pdb \
    --codon-times assets/csp/codon_dwell_times/yeast/yeast_codon_dwell_times_OBrien.txt \
    --mode slowest