Evidence map›Paper›PMID 25505094›Full record

ArticleBioinformatics (Oxford, England)2015

Detection of circular permutations within protein structures using CE-CP.

Spencer E Bliven, Philip E Bourne, Andreas Prlić

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.

0numbers the graph read from it
0cells of the map it votes in
19citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

19 citing papers in PubMed.

  1. Systematic discovery of circular permutations across the protein universe using CIRPIN.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  2. Article
  3. Article
  4. Article
  5. BEST: Basic Embedding Search Tool Enhancing Discovery of Novel Enzyme.Interdisciplinary sciences, computational life sciences · 2026
    Article
  6. Article
  7. Exploring the Structural Lexicon of the Proteome via Metric Geometry.bioRxiv : the preprint server for biology · 2025
    Article
  8. Article
  9. Article
  10. Detection of circular permutations by Protein Language Models.Computational and structural biotechnology journal · 2025
    Article
  11. Article
  12. SeqCP: A sequence-based algorithm for searching circularly permuted proteins.Computational and structural biotechnology journal · 2023
    Article
  13. Ribonuclease T2 represents a distinct circularly permutated version of the BECR RNases.Protein science : a publication of the Protein Society · 2023
    Article
  14. Article
  15. Article
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  18. Review
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

3 authors.

Spencer E BlivenBioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
Philip E BourneBioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.
Andreas PrlićBioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA 92093, USA, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA and RCSB Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA.

Funding

GRADUATE TRAINING PROGRAM IN BIONFORMATICST32GM008806 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BAFNA, VINEET, REN, BING · 2001 to 2020
$6.2M
Structural Bioinformatics, Systems Pharmacology and Scholarly CommunicationZIALM000928 · NLM · NATIONAL LIBRARY OF MEDICINE · PI BOURNE, PHILIP · 2015 to 2016
$1.3M
NIGMS NIH HHS T32GM8806
6 · The paper itself

Abstract

motivationCircular permutation is an important type of protein rearrangement. Natural circular permutations have implications for protein function, stability and evolution. Artificial circular permutations have also been used for protein studies. However, such relationships are difficult to detect for many sequence and structure comparison algorithms and require special consideration.

resultsWe developed a new algorithm, called Combinatorial Extension for Circular Permutations (CE-CP), which allows the structural comparison of circularly permuted proteins. CE-CP was designed to be user friendly and is integrated into the RCSB Protein Data Bank. It was tested on two collections of circularly permuted proteins. Pairwise alignments can be visualized both in a desktop application or on the web using Jmol and exported to other programs in a variety of formats. AVAILABILITY AND IMPLEMENTATION: The CE-CP algorithm can be accessed through the RCSB website at http://www.rcsb.org/pdb/workbench/workbench.do. Source code is available under the LGPL 2.1 as part of BioJava 3 (http://biojava.org; http://github.com/biojava/biojava). CONTACT: sbliven@ucsd.edu or info@rcsb.org.

Indexed as

AlgorithmsDatabases, ProteinStructural Homology, ProteinComputational BiologyDynaminsHumansProgramming LanguagesProtein Structure, TertiarySequence Analysis, ProteinDynamins

Identifiers

PMID25505094
PMCPMC4393524

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.