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Cited by 50RNA and protein synthesis mechanismsGenomics and Phylogenetic StudiesRNA Research and Splicing

Transimulation - Protein Biosynthesis Web Service

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Siwiak, Marlena, Zielenkiewicz, Piotr·2013·PLoS ONE
DOI 10.1371/journal.pone.0073943PMC PMC3764131
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Abstract

Although translation is the key step during gene expression, it remains poorly characterized at the level of individual genes. For this reason, we developed Transimulation - a web service measuring translational activity of genes in three model organisms: Escherichia coli, Saccharomyces cerevisiae and Homo sapiens. The calculations are based on our previous computational model of translation and experimental data sets. Transimulation quantifies mean translation initiation and elongation time (expressed in SI units), and the number of proteins produced per transcript. It also approximates the number of ribosomes that typically occupy a transcript during translation, and simulates their propagation. The simulation of ribosomes' movement is interactive and allows modifying the coding sequence on the fly. It also enables uploading any coding sequence and simulating its translation in one of three model organisms. In such a case, ribosomes propagate according to mean codon elongation times of the host organism, which may prove useful for heterologous expression. Transimulation was used to examine evolutionary conservation of translational parameters of orthologous genes. Transimulation may be accessed at http://nexus.ibb.waw.pl/Transimulation (requires Java version 1.7 or higher). Its manual and source code, distributed under the GPL-2.0 license, is freely available at the website.

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  • Reported values for the mean time for translation initiation per mRNA vary widely, with a minimum of 1 second and median of 15 seconds.

    “Reported values for the mean time for translation initiation per mRNA vary widely, with a minimum of 1 second and median of 15 seconds.”

    From Bringing the genetically minimal cell to life on a computer in 4D (2026) · cites this paper as [90]

    Table 1 in Results > Translational Model for Three Organisms reports a minimum initiation time of 1 second for human (HeLa) transcripts, but their median is 4 seconds. The 15-second median is for E. coli, whose minimum is 2 seconds. The sentence combines values from different organisms without saying so. (LLM, conf=0.93)

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Cited by

Sorted by citations

Authors
Siwiak, M., & Zielenkiewicz, P.
Affiliations
Institute of Biochemistry and Biophysics, Polish Academy of Sciences (PL)
Corresponding author
Zielenkiewicz, Piotr
ORCID
Zielenkiewicz, Piotr
Venue
PLoS ONE
Publisher
Public Library of Science (PLoS)
Published
2013-09-05
Volume
8
Issue
9
Pages
e73943
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0073943
PMC
PMC3764131
OpenAlex
W2022393880
Cited by
50
References
7
Citations by year
2026: 1 · 2025: 4 · 2024: 1 · 2023: 3 · 2022: 3 · 2021: 7 · 2020: 5 · 2019: 7 · 2018: 5 · 2017: 4 · 2016: 4 · 2015: 5 · 2014: 1
FWCI
1.49
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • Europe PMC (PubMed Central) (publishedVersion, other-oa)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Figshare (submittedVersion, cc-by)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
protein synthesis, translation (biology), translational activity, translation initiation, translation elongation, heterologous expression, orthologs, Escherichia coli, Saccharomyces cerevisiae, human, web services
MeSH terms
Escherichia coli, Humans, Proteins, Saccharomyces cerevisiae, Protein Biosynthesis, Web Browser

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