ArticleProtein science : a publication of the Protein Society2018
%MinMax: A versatile tool for calculating and comparing synonymous codon usage and its impact on protein folding.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- Enhancing protein expression in humans through codon optimization with transformer and contrastive learning.Molecular therapy. Nucleic acids · 2026Article
- Efficient experimental characterization of the GPCRome via deep receptor scanning.Nature communications · 2026Article
- Discovery and validation of ASG1 as a novel determinant of NaCl tolerance in the yeast Saccharomyces cerevisiae through iterative crossing.G3 (Bethesda, Md.) · 2026Article
- Deep Receptor Scanning Reveals General Sequence Constraints on GPCR Biosynthesis.bioRxiv : the preprint server for biology · 2025Article
- Article
- A generative language model decodes contextual constraints on codon choice for mRNA design.bioRxiv : the preprint server for biology · 2025Article
- Investigating the impact of synonymous gene recoding on a recombinantly expressed monoclonal antibody under different process parameters.Bioengineering & translational medicine · 2025Article
- The differential effect of SARS-CoV-2 NSP1 on mRNA translation and stability reveals new insights linking ribosome recruitment, codon usage, and virus evolution.Nucleic acids research · 2025Article
- Ramp Sequence May Explain Synonymous Variant Association with Alzheimer's Disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (PILRA).Biomedicines · 2025Article
- Less is more: slow-codon windows enhance eGFP mRNA resilience against RNA interference.Journal of the Royal Society, Interface · 2025Article
- Ramp sequence may explain synonymous variant association with Alzheimer's disease in the Paired Immunoglobulin-like Type 2 Receptor Alpha (bioRxiv : the preprint server for biology · 2025Article
- Upstream open reading frames repress the translation from the iab-8 RNA.PLoS genetics · 2024Article
- Profiling expression strategies for a type III polyketide synthase in a lysate-based, cell-free system.Scientific reports · 2024Article
- Modifications of the 5' region of the CASPONMicrobial cell factories · 2024Article
- Codon-optimization in gene therapy: promises, prospects and challenges.Frontiers in bioengineering and biotechnology · 2024Review
- An exploratory in silico comparison of open-source codon harmonization tools.Microbial cell factories · 2023Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- A Short Tale of the Origin of Proteins and Ribosome Evolution.Microorganisms · 2022Review
- Synonymous ADAMTS13 variants impact molecular characteristics and contribute to variability in active protein abundance.Blood advances · 2022Article
- Protocol to identify host-viral protein interactions between coagulation-related proteins and their genetic variants with SARS-CoV-2 proteins.STAR protocols · 2022Article
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Abstract
Most amino acids can be encoded by more than one synonymous codon, but these are rarely used with equal frequency. In many coding sequences the usage patterns of rare versus common synonymous codons is nonrandom and under selection. Moreover, synonymous substitutions that alter these patterns can have a substantial impact on the folding efficiency of the encoded protein. This has ignited broad interest in exploring synonymous codon usage patterns. For many protein chemists, biophysicists and structural biologists, the primary motivation for codon analysis is identifying and preserving usage patterns most likely to impact high-yield production of functional proteins. Here we describe the core functions and new features of %MinMax, a codon usage calculator freely available as a web-based portal and downloadable script (http://www.codons.org). %MinMax evaluates the relative usage frequencies of the synonymous codons used to encode a protein sequence of interest and compares these results to a rigorous null model. Crucially, for analyzing codon usage in common host organisms %MinMax requires only the coding sequence as input; with a user-input codon frequency table, %MinMax can be used to evaluate synonymous codon usage patterns for any coding sequence from any fully sequenced genome. %MinMax makes no assumptions regarding the impact of transfer ribonucleic acid concentrations or other molecular-level interactions on translation rates, yet its output is sufficient to predict the effects of synonymous codon substitutions on cotranslational folding mechanisms. A simple calculation included within %MinMax can be used to harmonize codon usage frequencies for heterologous gene expression.
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