ReviewCurrent opinion in structural biology2020
Practically useful protein-design methods combining phylogenetic and atomistic calculations.
Review in Current opinion in structural biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- Revolutionizing oncology: the role of Artificial Intelligence (AI) as an antibody design, and optimization tools.Biomarker research · 2025Review
- Continuous Biosensing to Monitor Acute Systemic Inflammation, a Diagnostic Need for Therapeutic Guidance.ACS sensors · 2025Review
- Addressing epistasis in the design of protein function.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Opportunities and challenges in design and optimization of protein function.Nature reviews. Molecular cell biology · 2024Review
- One-shot design elevates functional expression levels of a voltage-gated potassium channel.Protein science : a publication of the Protein Society · 2024Article
- Enhancing the endo-activity of the thermophilic chitinase to yield chitooligosaccharides with high degrees of polymerization.Bioresources and bioprocessing · 2024Article
- Designed active-site library reveals thousands of functional GFP variants.Nature communications · 2023Article
- Automated optimisation of solubility and conformational stability of antibodies and proteins.Nature communications · 2023Article
- Repertoire of Computationally Designed Peroxygenases for Enantiodivergent C-H Oxyfunctionalization Reactions.Journal of the American Chemical Society · 2023Article
- Funneling modulatory peptide design with generative models: Discovery and characterization of disruptors of calcineurin protein-protein interactions.PLoS computational biology · 2023Article
- Engineering functional thermostable proteins using ancestral sequence reconstruction.The Journal of biological chemistry · 2022Review
- Assessing and enhancing foldability in designed proteins.Protein science : a publication of the Protein Society · 2022Article
- Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences.Journal of the American Chemical Society · 2022Article
- What Have We Learned from Design of Function in Large Proteins?Biodesign research · 2022Review
- Data-driven computational protein design.Current opinion in structural biology · 2021Review
- Computationally designed pyocyanin demethylase acts synergistically with tobramycin to kill recalcitrantProceedings of the National Academy of Sciences of the United States of America · 2021Article
- Engineered Enzymes Enable Selective N-Alkylation of Pyrazoles With Simple Haloalkanes.Angewandte Chemie (International ed. in English) · 2021Article
- The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes.Protein science : a publication of the Protein Society · 2021Article
- The evolving art of creating genetic diversity: From directed evolution to synthetic biology.Biotechnology advancesReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Our ability to design new or improved biomolecular activities depends on understanding the sequence-function relationships in proteins. The large size and fold complexity of most proteins, however, obscure these relationships, and protein-optimization methods continue to rely on laborious experimental iterations. Recently, a deeper understanding of the roles of stability-threshold effects and biomolecular epistasis in proteins has led to the development of hybrid methods that combine phylogenetic analysis with atomistic design calculations. These methods enable reliable and even single-step optimization of protein stability, expressibility, and activity in proteins that were considered outside the scope of computational design. Furthermore, ancestral-sequence reconstruction produces insights on missing links in the evolution of enzymes and binders that may be used in protein design. Through the combination of phylogenetic and atomistic calculations, the long-standing goal of general computational methods that can be universally applied to study and optimize proteins finally seems within reach.
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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.