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PredictProtein was the first Internet server for protein predictions. It pioneered combining evolutionary information and machine learning. Given a protein sequence as input, the server outputs multiple sequence alignments, predictions of protein structure in 1D and 2D (secondary structure, solvent accessibility, transmembrane segments, disordered regions, protein flexibility, and disulfide bridges) and predictions of protein function (functional effects of sequence variation or point mutations, Gene Ontology (GO) terms, subcellular localization, and protein-, RNA-, and DNA binding). PredictProtein's infrastructure has moved to the LCSB increasing throughput; the use of MMseqs2 sequence search reduced runtime five-fold (apparently without lowering performance of prediction methods); user interface elements improved usability, and new prediction methods were added. PredictProtein recently included predictions from deep learning embeddings (GO and secondary structure) and a method for the prediction of proteins and residues binding DNA, RNA, or other proteins. PredictProtein.org aspires to provide reliable predictions to computational and experimental biologists alike. All scripts and methods are freely available for offline execution in high-throughput settings.<\/jats:p>","DOI":"10.1093\/nar\/gkab354","type":"journal-article","created":{"date-parts":[[2021,5,11]],"date-time":"2021-05-11T03:20:33Z","timestamp":1620703233000},"page":"W535-W540","source":"Crossref","is-referenced-by-count":234,"title":["PredictProtein - Predicting Protein Structure and Function for 29 Years"],"prefix":"10.1093","volume":"49","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6103-3306","authenticated-orcid":false,"given":"Michael","family":"Bernhofer","sequence":"first","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"},{"name":"TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4650-6181","authenticated-orcid":false,"given":"Christian","family":"Dallago","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"},{"name":"TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany"}]},{"given":"Tim","family":"Karl","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6532-5880","authenticated-orcid":false,"given":"Venkata","family":"Satagopam","sequence":"additional","affiliation":[{"name":"Luxembourg Centre For Systems Biomedicine (LCSB), University of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg"},{"name":"ELIXIR Luxembourg (ELIXIR-LU) Node, University of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg"}]},{"given":"Michael","family":"Heinzinger","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"},{"name":"TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany"}]},{"given":"Maria","family":"Littmann","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"},{"name":"TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany"}]},{"given":"Tobias","family":"Olenyi","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1790-8536","authenticated-orcid":false,"given":"Jiajun","family":"Qiu","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"},{"name":"Department of Otolaryngology Head & Neck Surgery, The Ninth People's Hospital & Ear Institute, School of Medicine & Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai Jiao Tong University, Shanghai, China"}]},{"given":"Konstantin","family":"Sch\u00fctze","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"}]},{"given":"Guy","family":"Yachdav","sequence":"additional","affiliation":[{"name":"TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology - i12, Boltzmannstr 3, 85748 Garching\/Munich, Germany"}]},{"given":"Haim","family":"Ashkenazy","sequence":"additional","affiliation":[{"name":"Department of Molecular Biology, Max Planck Institute for Developmental Biology, T\u00fcbingen, Germany"},{"name":"The Shmunis School of Biomedicine and Cancer Research, George S. 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