EMBER—Embedding Multiple Molecular Fingerprints for Virtual Screening

Isabella Mendolia, Roberto Pirrone, Salvatore Contino, Ugo Perricone, Giada De Simone

Research output: Contribution to journalArticlepeer-review


In recent years, the debate in the field of applications of Deep Learning to Virtual Screening has focused on the use of neural embeddings with respect to classical descriptors in order to encode both structural and physical properties of ligands and/or targets. The attention on embeddings with the increasing use of Graph Neural Networks aimed at overcoming molecular fingerprints that are short range embeddings for atomic neighborhoods. Here, we present EMBER, a novel molecular embedding made by seven molecular fingerprints arranged as different “spectra” to describe the same molecule, and we prove its effectiveness by using deep convolutional architecture that assesses ligands’ bioactivity on a data set containing twenty protein kinases with similar binding sites to CDK1. The data set itself is presented, and the architecture is explained in detail along with its training procedure. We report experimental results and an explainability analysis to assess the contribution of each fingerprint to different targets.
Original languageEnglish
Number of pages17
JournalInternational Journal of Molecular Sciences
Publication statusPublished - 2022

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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