ArticleBiophysical journal2012
A comparison of genotype-phenotype maps for RNA and proteins.
Article in Biophysical journal, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 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
25 citing papers in PubMed.
- Predicting RNA and Protein:RNA Complexes with AlphaFold: Possibilities, Limitations, and Practical Guidelines.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Evolution takes multiple paths to evolvability when facing environmental change.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Boltzmann distributions of molecular structures predict likely changes through random mutations.Biophysical journal · 2023Article
- Towards an engineering theory of evolution.Nature communications · 2021Review
- On the evolution and development of morphological complexity: A view from gene regulatory networks.PLoS computational biology · 2021Article
- Neutral components show a hierarchical community structure in the genotype-phenotype map of RNA secondary structure.Journal of the Royal Society, Interface · 2020Article
- Using small samples to estimate neutral component size and robustness in the genotype-phenotype map of RNA secondary structure.Journal of the Royal Society, Interface · 2020Article
- On the networked architecture of genotype spaces and its critical effects on molecular evolution.Open biology · 2018Review
- Phenotypes can be robust and evolvable if mutations have non-local effects on sequence constraints.Journal of the Royal Society, Interface · 2018Article
- Structural properties of genotype-phenotype maps.Journal of the Royal Society, Interface · 2017Review
- Distribution of genotype network sizes in sequence-to-structure genotype-phenotype maps.Journal of the Royal Society, Interface · 2017Article
- The potential for non-adaptive origins of evolutionary innovations in central carbon metabolism.BMC systems biology · 2016Article
- Genetic Correlations Greatly Increase Mutational Robustness and Can Both Reduce and Enhance Evolvability.PLoS computational biology · 2016Article
- The organization of biological sequences into constrained and unconstrained parts determines fundamental properties of genotype-phenotype maps.Journal of the Royal Society, Interface · 2015Article
- Intramolecular phenotypic capacitance in a modular RNA molecule.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms.Annual review of ecology, evolution, and systematics · 2014Article
- Empirical fitness landscapes and the predictability of evolution.Nature reviews. Genetics · 2014Review
- A tractable genotype-phenotype map modelling the self-assembly of protein quaternary structure.Journal of the Royal Society, Interface · 2014Article
- The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima.PloS one · 2014Article
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
The relationship between the genotype (sequence) and the phenotype (structure) of macromolecules affects their ability to evolve new structures and functions. We here compare the genotype space organization of proteins and RNA molecules to identify differences that may affect this ability. To this end, we computationally study the genotype-phenotype relationship for short RNA and lattice proteins of a reduced monomer alphabet size, to make exhaustive analysis and direct comparison of their genotype spaces feasible. We find that many fewer protein molecules than RNA molecules fold, but they fold into many more structures than RNA. In consequence, protein phenotypes have smaller genotype networks whose member genotypes tend to be more similar than for RNA phenotypes. Neighborhoods in sequence space of a given radius around an RNA molecule contain more novel structures than for protein molecules. We compare this property to evidence from natural RNA and protein molecules, and conclude that RNA genotype space may be more conducive to the evolution of new structure phenotypes.
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.