ArticleNature chemical biology2016
De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.
Article in Nature chemical biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 118 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
118 citing papers in PubMed.
- HURDLER: a cloning method to overcome length limits in designed repeat proteins.Nucleic acids research · 2026Article
- Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.Nature chemical biology · 2026Article
- Stability and cooperativity in chimeric de novo TIM barrels via quarter swapping.Protein science : a publication of the Protein Society · 2026Article
- The Borderlands of Foldability: Lessons from Simplified Proteins.Trends in chemistry · 2026Article
- Review
- Designing de novo TIM barrels: insights into stabilization, diversification, and functionalization strategies.Biochemical Society transactions · 2026Review
- Evaluating zero-shot prediction of monomeric protein design success by AlphaFold, ESMFold, and ProteinMPNN.Protein science : a publication of the Protein Society · 2026Article
- Protein engineering: status report.Protein engineering, design & selection : PEDS · 2026Review
- The Roles of EDA2R in Ageing and Disease.Aging cell · 2025Review
- Article
- Article
- Large-scale energy decomposition for the analysis of protein stability.Cell stress & chaperones · 2025Article
- Structure-based protein and small molecule generation using EGNN and diffusion models: A comprehensive review.Computational and structural biotechnology journal · 2024Review
- Exploration of the hierarchical assembly space of collagen-like peptides beyond the triple helix.Nature communications · 2024Article
- A De Novo Metalloenzyme for Cerium Photoredox Catalysis.Journal of the American Chemical Society · 2024Article
- AI in cellular engineering and reprogramming.Biophysical journal · 2024Review
- Article
- De novo design of buttressed loops for sculpting protein functions.Nature chemical biology · 2024Article
- Opportunities and challenges in design and optimization of protein function.Nature reviews. Molecular cell biology · 2024Review
- Article
58 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
Authors and funding
6 authors.
Funding
Abstract
Despite efforts for over 25 years, de novo protein design has not succeeded in achieving the TIM-barrel fold. Here we describe the computational design of four-fold symmetrical (β/α)8 barrels guided by geometrical and chemical principles. Experimental characterization of 33 designs revealed the importance of side chain-backbone hydrogen bonds for defining the strand register between repeat units. The X-ray crystal structure of a designed thermostable 184-residue protein is nearly identical to that of the designed TIM-barrel model. PSI-BLAST searches do not identify sequence similarities to known TIM-barrel proteins, and sensitive profile-profile searches indicate that the design sequence is distant from other naturally occurring TIM-barrel superfamilies, suggesting that Nature has sampled only a subset of the sequence space available to the TIM-barrel fold. The ability to design TIM barrels de novo opens new possibilities for custom-made enzymes.
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.