ArticleThe journal of physical chemistry. B2017
Why Is There a Glass Ceiling for Threading Based Protein Structure Prediction Methods?
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 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
7 citing papers in PubMed.
- Contact-Assisted Threading in Low-Homology Protein Modeling.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Homology Modeling in the Twilight Zone: Improved Accuracy by Sequence Space Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Toward the solution of the protein structure prediction problem.The Journal of biological chemistry · 2021Review
- The role of local versus nonlocal physicochemical restraints in determining protein native structure.Current opinion in structural biology · 2021Review
- Computational Methods for the Elucidation of Protein Structure and Interactions.Methods in molecular biology (Clifton, N.J.) · 2021Review
- DESTINI: A deep-learning approach to contact-driven protein structure prediction.Scientific reports · 2019Article
- MELD × MD Folds Nonthreadables, Giving Native Structures and Populations.Journal of chemical theory and computation · 2018Article
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
Abstract
Despite their different implementations, comparison of the best threading approaches to the prediction of evolutionary distant protein structures reveals that they tend to succeed or fail on the same protein targets. This is true despite the fact that the structural template library has good templates for all cases. Thus, a key question is why are certain protein structures threadable while others are not. Comparison with threading results on a set of artificial sequences selected for stability further argues that the failure of threading is due to the nature of the protein structures themselves. Using a new contact map based alignment algorithm, we demonstrate that certain folds are highly degenerate in that they can have very similar coarse grained fractions of native contacts aligned and yet differ significantly from the native structure. For threadable proteins, this is not the case. Thus, contemporary threading approaches appear to have reached a plateau, and new approaches to structure prediction are required.
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.