ArticleMolecular systems biology2021
Exploring amino acid functions in a deep mutational landscape.
Article in Molecular systems biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
38 citing papers in PubMed.
- Toward Advanced Quantitative Prediction of Missense Variant Effects.International journal of molecular sciences · 2026Article
- Systematic and proactive evaluation of AIRE missense variant effects.American journal of human genetics · 2026Article
- Phylogenetic and biological features of severe fever with thrombocytopenia syndrome virus from multi-species infections in eastern China.Microbiology spectrum · 2026Article
- How far can you go? Extrapolating values of catalytic activity from known protein landscapes in natural and directed evolution.Chemical Society reviews · 2026Review
- Article
- Predicting antifolate resistance in the unculturable fungal pathogen Pneumocystis jirovecii.PLoS genetics · 2026Article
- Supervised learning of protein variant effects across large-scale mutagenesis datasets.Protein science : a publication of the Protein Society · 2026Article
- DEX: a consensus-based amino acid exchangeability measure for improved codon substitution modelling.bioRxiv : the preprint server for biology · 2026Article
- Precise Construction of an Antimicrobial Peptide Targeting Bacterial Cell Membranes Derived From Natural Peptides.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Accurate variant effect estimation in FACS-based deep mutational scanning data with Lilace.Genome biology · 2026Article
- Evolutionary analysis ofFrontiers in plant science · 2026Article
- Rosace-AA: enhancing interpretation of deep mutational scanning data with amino acid substitution and position-specific insights.Bioinformatics advances · 2026Article
- Systematic and proactive evaluation of AIRE missense variant effects.bioRxiv : the preprint server for biology · 2025Article
- Landscapes of missense variant impact for human superoxide dismutase 1.American journal of human genetics · 2025Article
- The Essentiality of Amino Acids in Healthiness and Disease State: Type II Diabetes as a Case Study.Food science & nutrition · 2025Review
- Deep mutational scanning reveals a de novo disulfide bond and combinatorial mutations for engineering thermostable myoglobin.Protein science : a publication of the Protein Society · 2025Article
- Article
- Deep indel mutagenesis reveals the impact of amino acid insertions and deletions on protein stability and function.Nature communications · 2025Article
- QAFI: a novel method for quantitative estimation of missense variant impact using protein-specific predictors and ensemble learning.Human genetics · 2025Article
- Prediction of the Trimer Protein Interface Residue Pair by CNN-GRU Model Based on Multi-Feature Map.Nanomaterials (Basel, Switzerland) · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Amino acids fulfil a diverse range of roles in proteins, each utilising its chemical properties in different ways in different contexts to create required functions. For example, cysteines form disulphide or hydrogen bonds in different circumstances and charged amino acids do not always make use of their charge. The repertoire of amino acid functions and the frequency at which they occur in proteins remains understudied. Measuring large numbers of mutational consequences, which can elucidate the role an amino acid plays, was prohibitively time-consuming until recent developments in deep mutational scanning. In this study, we gathered data from 28 deep mutational scanning studies, covering 6,291 positions in 30 proteins, and used the consequences of mutation at each position to define a mutational landscape. We demonstrated rich relationships between this landscape and biophysical or evolutionary properties. Finally, we identified 100 functional amino acid subtypes with a data-driven clustering analysis and studied their features, including their frequencies and chemical properties such as tolerating polarity, hydrophobicity or being intolerant of charge or specific amino acids. The mutational landscape and amino acid subtypes provide a foundational catalogue of amino acid functional diversity, which will be refined as the number of studied protein positions increases.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.