ArticleScientific reports2017
Studies of global and local entanglements of individual protein chains using the concept of knotoids.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 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
14 citing papers in PubMed.
- Theta-curves in proteins.Protein science : a publication of the Protein Society · 2024Article
- Folding kinetics of an entangled protein.PLoS computational biology · 2023Article
- Entangled Motifs in Membrane Protein Structures.International journal of molecular sciences · 2023Article
- Geometric Predictors of Knotted and Linked Arcs.ACS polymers Au · 2022Article
- Topological dynamics of an intrinsically disordered N-terminal domain of the human androgen receptor.Protein science : a publication of the Protein Society · 2022Article
- Knot polynomials of open and closed curves.Proceedings. Mathematical, physical, and engineering sciences · 2020Article
- Knot_pull-python package for biopolymer smoothing and knot detection.Bioinformatics (Oxford, England) · 2020Article
- Article
- Folding Rate Optimization Promotes Frustrated Interactions in Entangled Protein Structures.International journal of molecular sciences · 2019Article
- Sequence and structural patterns detected in entangled proteins reveal the importance of co-translational folding.Scientific reports · 2019Article
- Topological descriptions of protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- KnotProt 2.0: a database of proteins with knots and other entangled structures.Nucleic acids research · 2019Article
- To Tie or Not to Tie? That Is the Question.Polymers · 2017Review
- Topological Models for Open-Knotted Protein Chains Using the Concepts of Knotoids and Bonded Knotoids.Polymers · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We study here global and local entanglements of open protein chains by implementing the concept of knotoids. Knotoids have been introduced in 2012 by Vladimir Turaev as a generalization of knots in 3-dimensional space. More precisely, knotoids are diagrams representing projections of open curves in 3D space, in contrast to knot diagrams which represent projections of closed curves in 3D space. The intrinsic difference with classical knot theory is that the generalization provided by knotoids admits non-trivial topological entanglement of the open curves provided that their geometry is frozen as it is the case for crystallized proteins. Consequently, our approach doesn't require the closure of chains into loops which implies that the geometry of analysed chains does not need to be changed by closure in order to characterize their topology. Our study revealed that the knotoid approach detects protein regions that were classified earlier as knotted and also new, topologically interesting regions that we classify as pre-knotted.
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.