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Peptides in chemical space

Type of publication Peer-reviewed
Publikationsform Original article (peer-reviewed)
Author Capecchi Alice, Reymond Jean-Louis,
Project Chemical Space Design of Small Molecules and Peptides
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Original article (peer-reviewed)

Journal Medicine in Drug Discovery
Volume (Issue) 9
Page(s) 100081 - 100081
Title of proceedings Medicine in Drug Discovery
DOI 10.1016/j.medidd.2021.100081

Open Access

URL http://doi.org/10.1016/j.medidd.2021.100081
Type of Open Access Publisher (Gold Open Access)

Abstract

Peptides, defined as sequences of amino acids up to approximately 50 residues in length, represent an extremely large reservoir of potentially bioactive compounds, referred to here as the peptide chemical space. Recent advances in computer hardware and software have led to a wide application of computational methods to explore this chemical space. Here, we review different in silico approaches including structure-based design, genetic algorithms, and machine learning. We also review the use of molecular fingerprints to sample virtual libraries and to visualize the peptide chemical space. Finally, we present an overview of the known peptide chemical space in form of an interactive map representing 40,531 peptides collected from eleven open-access peptide and peptide-containing databases, accessible at https://tm.gdb.tools/map4/peptide_databases_tmap/. These peptides are displayed as TMAP (Tree-Map) according to their molecular fingerprint similarity computed using MAP4, a MinHashed atom pair fingerprint well suited to analyze large molecules.
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