{rfName}
A

Indexed in

License and use

Citations

2

Altmetrics

Analysis of institutional authors

Marabini RAuthorCarazo JmAuthor

Share

October 9, 2023
Publications
>
Article
Hybrid Gold

A new algorithm for particle weighted subtraction to decrease signals from unwanted components in single particle analysis

Publicated to:JOURNAL OF STRUCTURAL BIOLOGY. 215 (4): 108024- - 2023-12-01 215(4), DOI: 10.1016/j.jsb.2023.108024

Authors: Fernández-Giménez E; Martínez MM; Marabini R; Strelak D; Sánchez-García R; Carazo JM; Sorzano COS

Affiliations

Astex Pharmaceut, 436 Cambridge Sci Pk, Cambridge CB4 0QA, England - Author
Astex Pharmaceuticals , University of Oxford - Author
CSIC - Centro Nacional de Biotecnologia (CNB) - Author
Ctr Nac Biotecnol CSIC, C Darwin 3, Madrid 28049, Spain - Author
Masaryk Univ, Inst Comp Sci, Botanicka 68a, Brno 60200, Czech Republic - Author
Masaryk University - Author
Univ Autonoma Madrid, E-28049 Madrid, Spain - Author
Univ Oxford, Dept Stat, 24-29 St Giles, Oxford OX1 3LB, England - Author
Universidad Autónoma de Madrid , CSIC - Centro Nacional de Biotecnologia (CNB) - Author
See more

Abstract

Single particle analysis (SPA) in cryo-electron microscopy (cryo-EM) is highly used to obtain the near-atomic structure of biological macromolecules. The current methods allow users to produce high-resolution maps from many samples. However, there are still challenging cases that require extra processing to obtain high resolution. This is the case when the macromolecule of the sample is composed of different components and we want to focus just on one of them. For example, if the macromolecule is composed of several flexible subunits and we are interested in a specific one, if it is embedded in a viral capsid environment, or if it has additional components to stabilize it, such as nanodiscs. The signal from these components, which in principle we are not interested in, can be removed from the particles using a projection subtraction method. Currently, there are two projection subtraction methods used in practice and both have some limitations. In fact, after evaluating their results, we consider that the problem is still open to new solutions, as they do not fully remove the signal of the components that are not of interest. Our aim is to develop a new and more precise projection subtraction method, improving the performance of state-of-the-art methods. We tested our algorithm with data from public databases and an in–house data set. In this work, we show that the performance of our algorithm improves the results obtained by others, including the localization of small ligands, such as drugs, whose binding location is unknown a priori.

Keywords

cryo-emligandnanodiscprojection subtractionspaCryo-emLigandNanodiscProjection subtractionSpaXmipp

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal JOURNAL OF STRUCTURAL BIOLOGY due to its progression and the good impact it has achieved in recent years, according to the agency Scopus (SJR), it has become a reference in its field. In the year of publication of the work, 2023, it was in position , thus managing to position itself as a Q1 (Primer Cuartil), in the category Structural Biology.

Independientemente del impacto esperado determinado por el canal de difusión, es importante destacar el impacto real observado de la propia aportación.

Según las diferentes agencias de indexación, el número de citas acumuladas por esta publicación hasta la fecha 2025-07-05:

  • Scopus: 1

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 2025-07-05:

  • 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: 9 (PlumX).

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.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://repositorio.uam.es/handle/10486/711543

Leadership analysis of institutional authors

This work has been carried out with international collaboration, specifically with researchers from: Czech Republic; Czechoslovakia; United Kingdom.

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 (Fernández-Giménez E) .