ArticleJournal of the Royal Society, Interface2008
How much of protein sequence space has been explored by life on Earth?
Article in Journal of the Royal Society, Interface, 2008. 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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Who cites it
41 citing papers in PubMed.
- Genetically encoded tools for tracking metabolites in live cells.Biochemical Society transactions · 2026Review
- Tools For Building Artificial Biological Nanostructures.ACS nano · 2026Review
- Descent from a common ancestor restricts exploration of protein sequence space.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Advances in Machine Learning Models for Predicting Enzyme Kinetic Parameters.Journal of chemical information and modeling · 2026Review
- Protein sequence modelling with Bayesian flow networks.Nature communications · 2025Article
- Limitations of sequence dissimilarity as a predictor of prokaryotic lineage.Open biology · 2025Review
- Integrating genetic algorithms and language models for enhanced enzyme design.Briefings in bioinformatics · 2024Article
- Fundamental constraints to the logic of living systems.Interface focus · 2024Review
- The genetic architecture of protein stability.Nature · 2024Article
- Analysis of proteins in the light of mutations.European biophysics journal : EBJ · 2024Review
- A survey of generative AI for de novo drug design: new frontiers in molecule and protein generation.Briefings in bioinformatics · 2024Article
- Accelerating Genetic Sensor Development, Scale-up, and Deployment Using Synthetic Biology.Biodesign research · 2024Article
- New advances in protein engineering for industrial applications: Key takeaways.Open life sciences · 2024Review
- Review
- Protein folding rate evolution upon mutations.Biophysical reviews · 2023Review
- Gaia as Solaris: An Alternative Default Evolutionary Trajectory.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2022Article
- High throughput and quantitative enzymology in the genomic era.Current opinion in structural biology · 2021Review
- Ancestral sequences of a large promiscuous enzyme family correspond to bridges in sequence space in a network representation.Journal of the Royal Society, Interface · 2021Article
- Navigating the amino acid sequence space between functional proteins using a deep learning framework.PeerJ. Computer science · 2021Article
- About the Protein Space Vastness.The protein journal · 2020Review
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We suggest that the vastness of protein sequence space is actually completely explorable during the populating of the Earth by life by considering upper and lower limits for the number of organisms, genome size, mutation rate and the number of functionally distinct classes of amino acids. We conclude that rather than life having explored only an infinitesimally small part of sequence space in the last 4 Gyr, it is instead quite plausible for all of functional protein sequence space to have been explored and that furthermore, at the molecular level, there is no role for contingency.
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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.