ReviewProtein science : a publication of the Protein Society2012
The interface of protein structure, protein biophysics, and molecular evolution.
Review in Protein science : a publication of the Protein Society, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
What it found
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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.
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Who cites it
119 citing papers in PubMed.
- Integrating evolutionary signals and predicted protein structure reveals localized molecular divergence in Cereus lineages.Genetica · 2026Article
- Selection for Folding Stability Predicts Observed Covariation Between Protein Positions in the PDB.Journal of molecular evolution · 2026Article
- Site-Specific Structure and Stability Constrained Substitution Models Improve Phylogenetic Inference.Systematic biology · 2026Article
- Characterizing Physicochemical Selection in Protein Evolution with Property-Informed Models (PRIME).bioRxiv : the preprint server for biology · 2026Article
- Accurate prediction of substitution rates at protein sites with a mutation-selection model.Scientific reports · 2025Article
- Article
- A systematic evaluation of the language-of-viral-escape model using multiple machine learning frameworks.Journal of the Royal Society, Interface · 2025Article
- Exploring the CNOT1(800-999) HEAT Domain and Its Interactions with Tristetraprolin (TTP) as Revealed by Hydrogen/Deuterium Exchange Mass Spectrometry.Biomolecules · 2025Article
- Structure-based self-supervised learning enables ultrafast protein stability prediction upon mutation.Innovation (Cambridge (Mass.)) · 2025Article
- Neutral drift upon threshold-like selection promotes variation in antibiotic resistance phenotype.Nature communications · 2024Article
- A core network in the SARS-CoV-2 nucleocapsid NTD mediates structural integrity and selective RNA-binding.Nature communications · 2024Article
- Reused Protein Segments Linked to Functional Dynamics.Molecular biology and evolution · 2024Article
- Mapping conformational changes on bispecific antigen-binding biotherapeutic by covalent labeling and mass spectrometry.Journal of pharmaceutical analysis · 2024Article
- The Effects of Codon Usage on Protein Structure and Folding.Annual review of biophysics · 2024Review
- Kinetic and dynamical properties of truncated hemoglobins of the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125.Protein science : a publication of the Protein Society · 2024Article
- Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2.eLife · 2024Article
- Article
- Extant Sequence Reconstruction: The Accuracy of Ancestral Sequence Reconstructions Evaluated by Extant Sequence Cross-Validation.Journal of molecular evolution · 2024Article
- Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- Selection among site-dependent structurally constrained substitution models of protein evolution by approximate Bayesian computation.Bioinformatics (Oxford, England) · 2024Article
59 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
33 authors.
Funding
Abstract
Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction.
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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.