BUSCA: an integrative web server to predict subcellular localization of proteins von Savojardo, Castrense, Martelli, Pier Luigi, Fariselli, Piero, Profiti, Giuseppe, Casadio, Rita

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INPS-MD: a web server to predict stability of protein variants from sequence and structure von Savojardo, Castrense, Fariselli, Piero, Martelli, Pier Luigi, Casadio, Rita

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GraphDTA: predicting drug–target binding affinity with graph neural networks von Nguyen, Thin, Le, Hang, Quinn, Thomas P, Nguyen, Tri, Le, Thuc Duy, Venkatesh, Svetha

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ProteinBERT: a universal deep-learning model of protein sequence and function von Brandes, Nadav, Ofer, Dan, Peleg, Yam, Rappoport, Nadav, Linial, Michal

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DeepSig: deep learning improves signal peptide detection in proteins von Savojardo, Castrense, Martelli, Pier Luigi, Fariselli, Piero, Casadio, Rita

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DeepMito: accurate prediction of protein sub-mitochondrial localization using convolutional neural networks von Savojardo, Castrense, Bruciaferri, Niccolò, Tartari, Giacomo, Martelli, Pier Luigi, Casadio, Rita

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Machine learning solutions for predicting protein–protein interactions von Casadio, Rita, Martelli, Pier Luigi, Savojardo, Castrense

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sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure von Yan, Ke, Lv, Hongwu, Guo, Yichen, Peng, Wei, Liu, Bin

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Structure-aware protein–protein interaction site prediction using deep graph convolutional network von Yuan, Qianmu, Chen, Jianwen, Zhao, Huiying, Zhou, Yaoqi, Yang, Yuedong

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PredGPI: a GPI-anchor predictor von Pierleoni, Andrea, Martelli, Pier Luigi, Casadio, Rita

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LightBBB: computational prediction model of blood–brain-barrier penetration based on LightGBM von Shaker, Bilal, Yu, Myeong-Sang, Song, Jin Sook, Ahn, Sunjoo, Ryu, Jae Yong, Oh, Kwang-Seok, Na, Dokyun

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ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning von Wei, Lesong, Ye, Xiucai, Sakurai, Tetsuya, Mu, Zengchao, Wei, Leyi

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A natural upper bound to the accuracy of predicting protein stability changes upon mutations von Montanucci, Ludovica, Martelli, Pier Luigi, Ben-Tal, Nir, Fariselli, Piero

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Functional annotations improve the predictive score of human disease-related mutations in proteins von Calabrese, Remo, Capriotti, Emidio, Fariselli, Piero, Martelli, Pier Luigi, Casadio, Rita

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MOVICS: an R package for multi-omics integration and visualization in cancer subtyping von Lu, Xiaofan, Meng, Jialin, Zhou, Yujie, Jiang, Liyun, Yan, Fangrong

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MVGCN: data integration through multi-view graph convolutional network for predicting links in biomedical bipartite networks von Fu, Haitao, Huang, Feng, Liu, Xuan, Qiu, Yang, Zhang, Wen

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Testing the Capability of Embedding-Based Alignments on the GST Superfamily Classification: The Role of Protein Length von Vazzana, Gabriele, Savojardo, Castrense, Martelli, Pier Luigi, Casadio, Rita

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MIB2: metal ion-binding site prediction and modeling server von Lu, Chih-Hao, Chen, Chih-Chieh, Yu, Chin-Sheng, Liu, Yen-Yi, Liu, Jia-Jun, Wei, Sung-Tai, Lin, Yu-Feng

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Humanization of antibodies using a machine learning approach on large-scale repertoire data von Marks, Claire, Hummer, Alissa M, Chin, Mark, Deane, Charlotte M

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amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool von Lawrence, Travis J, Carper, Dana L, Spangler, Margaret K, Carrell, Alyssa A, Rush, Tomás A, Minter, Stephen J, Weston, David J, Labbé, Jessy L

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