ArticlePloS one2013
Transimulation - protein biosynthesis web service.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 52 citations in OpenAlex.
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- A computational spatial whole-Cell model for hepatitis B viral infection and drug interactions.Scientific reports · 2023Article
- A kinetic dichotomy between mitochondrial and nuclear gene expression drives OXPHOS biogenesis.bioRxiv : the preprint server for biology · 2023Article
- Stochastic dynamics and ribosome-RNAP interactions in transcription-translation coupling.Biophysical journal · 2023Article
- Using Models to (Re-)Design Synthetic Circuits.Methods in molecular biology (Clifton, N.J.) · 2021Article
- High Transcriptional Error Rates Vary as a Function of Gene Expression Level.Genome biology and evolution · 2020Article
- Models of protein production along the cell cycle: An investigation of possible sources of noise.PloS one · 2020Article
- Translational Control by Ribosome Pausing in Bacteria: How a Non-uniform Pace of Translation Affects Protein Production and Folding.Frontiers in microbiology · 2020Review
- Addressing Non-linear System Dynamics of Single-Strand RNA Virus-Host Interaction.Frontiers in microbiology · 2020Article
- Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises.Frontiers in microbiology · 2020Review
- Homeostasis in the Central Dogma of molecular biology: the importance of mRNA instability.RNA biology · 2019Article
- Article
- Optimizing the dynamics of protein expression.Scientific reports · 2019Article
- Intracellular Hepatitis C Virus Modeling Predicts Infection Dynamics and Viral Protein Mechanisms.Journal of virology · 2018Article
- Translation initiation in bacterial polysomes through ribosome loading on a standby site on a highly translated mRNA.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Genome scale analysis of Escherichia coli with a comprehensive prokaryotic sequence-based biophysical model of translation initiation and elongation.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.