ArticlePeerJ2013
How long is a piece of loop?
Article in PeerJ, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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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.
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Who cites it
13 citing papers in PubMed.
- A functional helix shuffled variant of the B domain of Staphylococcus aureus.Protein science : a publication of the Protein Society · 2025Article
- Physicochemical, functional, and evolutionary characteristics of protein loop regions in human andBiophysics and physicobiology · 2025Article
- Autoinhibition and relief mechanisms for MICAL monooxygenases in F-actin disassembly.Nature communications · 2024Article
- Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation.The journal of physical chemistry letters · 2024Article
- Sequence-independent activity of a predicted long disordered segment of the human papillomavirus type 16 L2 capsid protein during virus entry.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Loop dynamics and the evolution of enzyme activity.Nature reviews. Chemistry · 2023Review
- Whole genome sequence analysis of CPV-2 isolates from 1998 to 2020.Virology journal · 2023Article
- Conformation-selective rather than avidity-based binding to tumor associated antigen derived peptide-MHC enables targeting of WT1-pMHC low expressing cancer cells by anti-WT1-pMHC/CD3 T cell engagers.Frontiers in immunology · 2023Article
- Vaccine design based on 16 epitopes of SARS-CoV-2 spike protein.Journal of medical virology · 2021Article
- Simple Selection Procedure to Distinguish between Static and Flexible Loops.International journal of molecular sciences · 2020Article
- The soluble loop BC region guides, but not dictates, the assembly of the transmembrane cytochrome b6.PloS one · 2017Article
- An amino acid code for irregular and mixed protein packing.Proteins · 2015Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Loops are irregular structures which connect two secondary structure elements in proteins. They often play important roles in function, including enzyme reactions and ligand binding. Despite their importance, their structure remains difficult to predict. Most protein loop structure prediction methods sample local loop segments and score them. In particular protein loop classifications and database search methods depend heavily on local properties of loops. Here we examine the distance between a loop's end points (span). We find that the distribution of loop span appears to be independent of the number of residues in the loop, in other words the separation between the anchors of a loop does not increase with an increase in the number of loop residues. Loop span is also unaffected by the secondary structures at the end points, unless the two anchors are part of an anti-parallel beta sheet. As loop span appears to be independent of global properties of the protein we suggest that its distribution can be described by a random fluctuation model based on the Maxwell-Boltzmann distribution. It is believed that the primary difficulty in protein loop structure prediction comes from the number of residues in the loop. Following the idea that loop span is an independent local property, we investigate its effect on protein loop structure prediction and show how normalised span (loop stretch) is related to the structural complexity of loops. Highly contracted loops are more difficult to predict than stretched loops.
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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.