标题/作者	年份
Learning the protein language: Evolution, structure, and function T Bepler, B Berger Cell systems 12 (6), 654-669. e3	2021
Deep learning in proteomics B Wen, WF Zeng, Y Liao, Z Shi, SR Savage, W Jiang, B Zhang Proteomics 20 (21-22), 1900335	2020
Joint constrained learning for event-event relation extraction H Wang, M Chen, H Zhang, D Roth arXiv preprint arXiv:2010.06727	2020
Embeddings from protein language models predict conservation and variant effects C Marquet, M Heinzinger, T Olenyi, C Dallago, K Erckert, M Bernhofer, ... Human genetics 141 (10), 1629-1647	2022
Comparative molecular dynamics study of the receptor-binding domains in SARS-CoV-2 and SARS-CoV and the effects of mutations on the binding affinity S Rezaei, Y Sefidbakht, V Uskoković Journal of Biomolecular Structure and Dynamics 40 (10), 4662-4681	2022
Mutations of SARS-CoV-2 RBD may alter its molecular structure to improve its infection efficiency AL Alaofi, M Shahid Biomolecules 11 (9), 1273	2021
Diagnostic prediction with sequence-of-sets representation learning for clinical events T Zhang, M Chen, AAT Bui Artificial Intelligence in Medicine: 18th International Conference on …	2020
Retrieving complex tables with multi-granular graph representation learning F Wang, K Sun, M Chen, J Pujara, P Szekely Proceedings of the 44th International ACM SIGIR Conference on Research and …	2021
EpitopeVec: linear epitope prediction using deep protein sequence embeddings A Bahai, E Asgari, MRK Mofrad, A Kloetgen, AC McHardy Bioinformatics 37 (23), 4517-4525	2021
PyPEF—an integrated framework for data-driven protein engineering NE Siedhoff, AM Illig, U Schwaneberg, MD Davari Journal of Chemical Information and Modeling 61 (7), 3463-3476	2021
Persistent spectral based ensemble learning (PerSpect-EL) for protein–protein binding affinity prediction JJ Wee, K Xia Briefings in Bioinformatics 23 (2), bbac024	2022
Recent advances in predicting protein–protein interactions with the aid of artificial intelligence algorithms S Li, S Wu, L Wang, F Li, H Jiang, F Bai Current Opinion in Structural Biology 73, 102344	2022
Drug-target interaction prediction with graph attention networks H Wang, G Zhou, S Liu, JY Jiang, W Wang arXiv preprint arXiv:2107.06099	2021
Implications of disease-related mutations at protein–protein interfaces D Xiong, D Lee, L Li, Q Zhao, H Yu Current Opinion in Structural Biology 72, 219-225	2022
Rosetta custom score functions accurately predict ΔΔ G of mutations at protein–protein interfaces using machine learning SR Shringari, S Giannakoulias, JJ Ferrie, EJ Petersson Chemical Communications 56 (50), 6774-6777	2020
Event-event relation extraction using probabilistic box embedding EJ Hwang, JY Lee, T Yang, D Patel, D Zhang, A McCallum Proceedings of the 60th Annual Meeting of the Association for Computational …	2022
Hom-complex-based machine learning (HCML) for the prediction of protein–protein binding affinity changes upon mutation X Liu, H Feng, J Wu, K Xia Journal of chemical information and modeling 62 (17), 3961-3969	2022
Multimodal pre-training model for sequence-based prediction of protein-protein interaction Y Xue, Z Liu, X Fang, F Wang Machine Learning in Computational Biology, 34-46	2022
Biomolecular topology: Modelling and analysis J Liu, KL Xia, J Wu, SST Yau, GW Wei Acta Mathematica Sinica, English Series 38 (10), 1901-1938	2022
LambdaPP: Fast and accessible protein‐specific phenotype predictions T Olenyi, C Marquet, M Heinzinger, B Kröger, T Nikolova, M Bernhofer, ... Protein Science 32 (1), e4524	2023

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