ReviewCurrent opinion in structural biology2014
Merging molecular mechanism and evolution: theory and computation at the interface of biophysics and evolutionary population genetics.
Review in Current opinion in structural biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 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
52 citing papers in PubMed, 106 citations in OpenAlex.
- 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
- Forecasting drug resistant HIV protease evolution.PLoS computational biology · 2026Article
- Predicting side chain conformations in folded proteins by AlphaFold: Perspective and challenges.Biophysical journal · 2025Article
- Using AlphaFold2 to Predict the Conformations of Side Chains in Folded Proteins.bioRxiv : the preprint server for biology · 2025Article
- Advances in Whole Genome Sequencing: Methods, Tools, and Applications in Population Genomics.International journal of molecular sciences · 2025Review
- Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2.eLife · 2024Article
- Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2.bioRxiv : the preprint server for biology · 2024Article
- Using machine learning to predict the effects and consequences of mutations in proteins.Current opinion in structural biology · 2023Review
- Microbial population dynamics decouple growth response from environmental nutrient concentration.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Contingency and Entrenchment of Drug-Resistance Mutations in HIV Viral Proteins.The journal of physical chemistry. B · 2022Article
- The evolution of the HIV-1 protease folding stability.Virus evolution · 2022Article
- Methodologies for Microbial Ancestral Sequence Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2022Review
- A thermodynamic model of protein structure evolution explains empirical amino acid substitution matrices.Protein science : a publication of the Protein Society · 2021Article
- ADDRESS: A Database of Disease-associated Human Variants Incorporating Protein Structure and Folding Stabilities.Journal of molecular biology · 2021Article
- Mi3-GPU: MCMC-based Inverse Ising Inference on GPUs for protein covariation analysis.Computer physics communications · 2021Article
- Exploring the sequence fitness landscape of a bridge between protein folds.PLoS computational biology · 2020Article
- Effect of Protein Structure on Evolution of Cotranslational Folding.Biophysical journal · 2020Article
- Effects of Single Mutations on Protein Stability Are Gaussian Distributed.Biophysical journal · 2020Article
- Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes.Genetics · 2020Article
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 at 1 institution in 1 country.
Funding
Abstract
The variation among sequences and structures in nature is both determined by physical laws and by evolutionary history. However, these two factors are traditionally investigated by disciplines with different emphasis and philosophy-molecular biophysics on one hand and evolutionary population genetics in another. Here, we review recent theoretical and computational approaches that address the crucial need to integrate these two disciplines. We first articulate the elements of these approaches. Then, we survey their contribution to our mechanistic understanding of molecular evolution, the polymorphisms in coding region, the distribution of fitness effects (DFE) of mutations, the observed folding stability of proteins in nature, and the distribution of protein folds in genomes.
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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.