{rfName}
Br

Indexed in

License and use

Icono OpenAccess

Citations

118

Altmetrics

Grant support

PhD scholarship from the Institute for Science and Innovation Flanders (IWT) (to P. V. and L. B.); Long-term exchange fellowship from the Research Foundation Flanders (FWO) (to P. V.); PhD scholarship from the EU grant Penelope FW6 (to E. V.). Funding from the EU grants 3D repertoire and the Spanish grant Centrosome3D. Funding for open access charge: EU grants 3D repertoire and the Spanish grant Centrosome3D.

Analysis of institutional authors

Vanhee, PeterAuthorVerschueren, ErikAuthorStricher, FrancoisAuthorSerrano, LuisCorresponding Author

Share

March 25, 2020
Publications
>
Article
Sí

BriX: a database of protein building blocks for structural analysis, modeling and design

Publicated to:Nucleic Acids Research. 39 D435-D442 - 2011-01-01 39(), DOI: 10.1093/nar/gkq972

Authors: Vanhee, P; Verschueren, E; Baeten, L; Stricher, F; Serrano, L; Rousseau, F; Schymkowitz, J

Affiliations

Flanders Inst Biotechnol VIB, VIB SWITCH Lab, B-1050 Brussels, Belgium - Author
Free Univ Brussels VUB, B-1050 Brussels, Belgium - Author
UPF, CRG, EMBL CRG Syst Biol Res Unit, Barcelona 08003, Spain - Author
UPF, CRG, ICREA, Barcelona 08003, Spain - Author

Abstract

High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches using small, recurrent protein fragments have been employed. Here we present two databases that provide a vast resource for implementing such fragment-based strategies. The BriX database contains fragments from over 7000 non-homologous proteins from the Astral collection, segmented in lengths from 4 to 14 residues and clustered according to structural similarity, summing up to a content of 2 million fragments per length. To overcome the lack of loops classified in BriX, we constructed the Loop BriX database of non-regular structure elements, clustered according to end-to-end distance between the regular residues flanking the loop. Both databases are available online (http://brix.crg.es) and can be accessed through a user-friendly web-interface. For high-throughput queries a web-based API is provided, as well as full database downloads. In addition, two exciting applications are provided as online services: (i) user-submitted structures can be covered on the fly with BriX classes, representing putative structural variation throughout the protein and (ii) gaps or low-confidence regions in these structures can be bridged with matching fragments.

Keywords

ClassificationEngineFinderFragmentsMotifsPdbSequencesServerStructure prediction

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Nucleic Acids Research due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2011, it was in position 26/290, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biochemistry & Molecular Biology.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 4.09, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-09, the following number of citations:

  • WoS: 42
  • Scopus: 38
  • Europe PMC: 30

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-07-09:

  • The use, from an academic perspective evidenced by the Altmetric agency indicator referring to aggregations made by the personal bibliographic manager Mendeley, gives us a total of: 103.
  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 106 (PlumX).

With a more dissemination-oriented intent and targeting more general audiences, we can observe other more global scores such as:

  • The Total Score from Altmetric: 3.
  • The number of mentions on Wikipedia: 1 (Altmetric).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Belgium.

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (VANHEE, PETER) .

the author responsible for correspondence tasks has been SERRANO PUBUL, LUIS.