TY - JOUR A1 - Anteghini, Marco A1 - Martins dos Santos, Vitor AP A1 - Saccenti, Edoardo T1 - PortPred: Exploiting deep learning embeddings of amino acid sequences for the identification of transporter proteins and their substrates JF - Journal of Cellular Biochemistry N2 - The physiology of every living cell is regulated at some level by transporter proteins which constitute a relevant portion of membrane-bound proteins and are involved in the movement of ions, small and macromolecules across bio-membranes. The importance of transporter proteins is unquestionable. The prediction and study of previously unknown transporters can lead to the discovery of new biological pathways, drugs and treatments. Here we present PortPred, a tool to accurately identify transporter proteins and their substrate starting from the protein amino acid sequence. PortPred successfully combines pre-trained deep learning-based protein embeddings and machine learning classification approaches and outperforms other state-of-the-art methods. In addition, we present a comparison of the most promising protein sequence embeddings (Unirep, SeqVec, ProteinBERT, ESM-1b) and their performances for this specific task. Y1 - 2023 U6 - https://doi.org/10.1002/jcb.30490 VL - 124 IS - 11 SP - 1665 EP - 1885 ER - TY - CHAP A1 - Anteghini, Marco A1 - Martins Dos Santos, Vitor T1 - Computational Approaches for Peroxisomal Protein Localization T2 - Peroxisomes N2 - Computational approaches are practical when investigating putative peroxisomal proteins and for sub-peroxisomal protein localization in unknown protein sequences. Nowadays, advancements in computational methods and Machine Learning (ML) can be used to hasten the discovery of novel peroxisomal proteins and can be combined with more established computational methodologies. Here, we explain and list some of the most used tools and methodologies for novel peroxisomal protein detection and localization. Y1 - 2023 SN - 978-1-0716-3047-1 U6 - https://doi.org/10.1007/978-1-0716-3048-8_29 VL - 2643 SP - 405 EP - 411 PB - Humana, New York ER -