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Grant support

We deeply thank Dr. P. Hapala for providing us with the code used to simulate the AFM images. We would like to acknowledge support from the Comunidad de Madrid Industrial Doctorate programme 2017 under reference number IND2017/IND-7793, Quasar Science Resources S.L., and the Spanish MINECO (project MAT2017-83273-R). P.P. and R.P. acknowledge support from the Spanish Ministry of Science and Innovation, through project PID2020-115864RB-I00 and the "Maria de Maeztu" Programme for Units of Excellence in R&D (CEX2018-000805-M). Computer time provided by the Red Espan~ola de Supercomputacion (RES) at the Finisterrae II Supercomputer is gratefully acknowledged.

Analysis of institutional authors

Romero-Muñiz CAuthorPou PAuthorPerez RCorresponding Author

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March 9, 2022
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QUAM-AFM: A Free Database for Molecular Identification by Atomic Force Microscopy

Publicated to:Journal of Chemical Information and Modeling. 62 (5): 1214-1223 - 2022-03-14 62(5), DOI: 10.1021/acs.jcim.1c01323

Authors: Carracedo-Cosme, Jaime; Romero-Muniz, Carlos; Pou, Pablo; Perez, Ruben

Affiliations

Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, E-28049 Madrid, Spain. - Author
Departamento de Física Aplicada I, Universidad de Sevilla, E-41012 Seville, Spain. - Author
Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, E-28049 Madrid, Spain. - Author
Quasar Sci Resources SL, E-28232 Las Rozas De Madrid, Spain - Author
Quasar Science Resources S.L., Camino de las Ceudas 2, E-28232 Las Rozas de Madrid, Spain. - Author
Univ Autonoma Madrid, Condensed Matter Phys Ctr IFIMAC, E-28049 Madrid, Spain - Author
Univ Autonoma Madrid, Dept Fis Teor Mat Condensada, E-28049 Madrid, Spain - Author
Univ Seville, Dept Fis Aplicada 1, E-41012 Seville, Spain - Author
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Abstract

This paper introduces Quasar Science Resources-Autonomous University of Madrid atomic force microscopy image data set (QUAM-AFM), the largest data set of simulated atomic force microscopy (AFM) images generated from a selection of 685,513 molecules that span the most relevant bonding structures and chemical species in organic chemistry. QUAM-AFM contains, for each molecule, 24 3D image stacks, each consisting of constant-height images simulated for 10 tip-sample distances with a different combination of AFM operational parameters, resulting in a total of 165 million images with a resolution of 256 × 256 pixels. The 3D stacks are especially appropriate to tackle the goal of the chemical identification within AFM experiments by using deep learning techniques. The data provided for each molecule include, besides a set of AFM images, ball-and-stick depictions, IUPAC names, chemical formulas, atomic coordinates, and map of atom heights. In order to simplify the use of the collection as a source of information, we have developed a graphical user interface that allows the search for structures by CID number, IUPAC name, or chemical formula.

Keywords

Drug combinationsImaging, three-dimensionalLidaprimMicroscopy, atomic forceSulfanilamidesTotal-energy calculationsTrimethoprim

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Journal of Chemical Information and Modeling 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, 2022, it was in position 11/60, thus managing to position itself as a Q1 (Primer Cuartil), in the category Chemistry, Medicinal.

From a relative perspective, and based on the normalized impact indicator calculated from World Citations provided by WoS (ESI, Clarivate), it yields a value for the citation normalization relative to the expected citation rate of: 2.38. This 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: ESI Nov 14, 2024)

This information is reinforced by other indicators of the same type, which, although dynamic over time and dependent on the set of average global citations at the time of their calculation, consistently position the work at some point among the top 50% most cited in its field:

  • Weighted Average of Normalized Impact by the Scopus agency: 1.82 (source consulted: FECYT Feb 2024)
  • Field Citation Ratio (FCR) from Dimensions: 2.82 (source consulted: Dimensions Jul 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-07-19, the following number of citations:

  • WoS: 10
  • Scopus: 10
  • Europe PMC: 5

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 2025-07-19:

  • 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: 17.
  • 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: 22 (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: 5.3.
  • The number of mentions on the social network X (formerly Twitter): 10 (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.
  • Assignment of a Handle/URN as an identifier within the deposit in the Institutional Repository: https://repositorio.uam.es/handle/10486/719714

Leadership analysis of institutional authors

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 (Carracedo-Cosme J) and Last Author (PEREZ PEREZ, RUBEN).

the author responsible for correspondence tasks has been PEREZ PEREZ, RUBEN.