Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

PredictProtein – Predicting Protein Structure and Function for 29 Years

View ORCID ProfileMichael Bernhofer, View ORCID ProfileChristian Dallago, Tim Karl, View ORCID ProfileVenkata Satagopam, View ORCID ProfileMichael Heinzinger, View ORCID ProfileMaria Littmann, Tobias Olenyi, View ORCID ProfileJiajun Qiu, View ORCID ProfileKonstantin Schütze, Guy Yachdav, View ORCID ProfileHaim Ashkenazy, Nir Ben-Tal, View ORCID ProfileYana Bromberg, Tatyana Goldberg, View ORCID ProfileLaszlo Kajan, View ORCID ProfileSean O’Donoghue, View ORCID ProfileChris Sander, View ORCID ProfileAndrea Schafferhans, View ORCID ProfileAvner Schlessinger, Gerrit Vriend, View ORCID ProfileMilot Mirdita, View ORCID ProfilePiotr Gawron, View ORCID ProfileWei Gu, View ORCID ProfileYohan Jarosz, View ORCID ProfileChristophe Trefois, View ORCID ProfileMartin Steinegger, View ORCID ProfileReinhard Schneider, View ORCID ProfileBurkhard Rost
doi: https://doi.org/10.1101/2021.02.23.432527
Michael Bernhofer
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
2TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Michael Bernhofer
  • For correspondence: christian.dallago@tum.de assistant@rostlab.org
Christian Dallago
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
2TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christian Dallago
  • For correspondence: christian.dallago@tum.de assistant@rostlab.org
Tim Karl
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: christian.dallago@tum.de assistant@rostlab.org
Venkata Satagopam
3Luxembourg Centre For Systems Biomedicine (LCSB), Univ of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
4ELIXIR Luxembourg (ELIXIR-LU) Node, University of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Venkata Satagopam
  • For correspondence: christian.dallago@tum.de assistant@rostlab.org
Michael Heinzinger
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
2TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Michael Heinzinger
Maria Littmann
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
2TUM Graduate School CeDoSIA, Boltzmannstr 11, 85748 Garching, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Maria Littmann
Tobias Olenyi
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jiajun Qiu
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
5Dept Otolaryngology Head & Neck Surgery, The Ninth People’s Hospital & Ear Inst, School of Medicine & Shanghai Key Laboratory of Translational Medicine on Ear and Nose Diseases, Shanghai Jiao Tong University, Shanghai, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jiajun Qiu
Konstantin Schütze
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Konstantin Schütze
Guy Yachdav
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Haim Ashkenazy
6Dept Molecular Biology, Max Planck Inst for Developmental Biology, Tübingen, Germany
7The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Haim Ashkenazy
Nir Ben-Tal
8Dept Biochemistry & Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, 69978 Tel Aviv, Israel
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yana Bromberg
9Dept Biochemistry and Microbiology, Rutgers Univ, New Brunswick, NJ 08901, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yana Bromberg
Tatyana Goldberg
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Laszlo Kajan
10Roche Polska Sp. z o.o., Domaniewska 39B, 02-672 Warsaw, Poland
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Laszlo Kajan
Sean O’Donoghue
11Garvan Inst Medical Research, Sydney, Australia
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Sean O’Donoghue
Chris Sander
12Dept Data Sciences, Dana-Farber Cancer Inst, Boston, MA 02215, USA
13Dept of Cell Biology, Harvard Medical School, Boston, MA 02215, USA
14Broad Inst of MIT and Harvard, Boston, MA 02142, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Chris Sander
Andrea Schafferhans
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
15HSWT (Hochschule Weihenstephan Triesdorf | University of Applied Sciences), Dept of Bioengineering Sciences, Am Hofgarten 10, 85354 Freising, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Andrea Schafferhans
Avner Schlessinger
16Dept of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Avner Schlessinger
Gerrit Vriend
17BIPS, Poblacion Baco, Mindoro, Philippines
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Milot Mirdita
18Quantitative and Computational Biology, Max Planck Inst for Biophysical Chemistry, Göttingen, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Milot Mirdita
Piotr Gawron
3Luxembourg Centre For Systems Biomedicine (LCSB), Univ of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Piotr Gawron
Wei Gu
3Luxembourg Centre For Systems Biomedicine (LCSB), Univ of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
4ELIXIR Luxembourg (ELIXIR-LU) Node, University of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Wei Gu
Yohan Jarosz
3Luxembourg Centre For Systems Biomedicine (LCSB), Univ of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
4ELIXIR Luxembourg (ELIXIR-LU) Node, University of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Yohan Jarosz
Christophe Trefois
3Luxembourg Centre For Systems Biomedicine (LCSB), Univ of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
4ELIXIR Luxembourg (ELIXIR-LU) Node, University of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Christophe Trefois
Martin Steinegger
19School of Biological Sciences, Seoul National University, Seoul, South Korea
20Artificial Intelligence Inst, Seoul National University, Seoul, South Korea
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Martin Steinegger
Reinhard Schneider
3Luxembourg Centre For Systems Biomedicine (LCSB), Univ of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
4ELIXIR Luxembourg (ELIXIR-LU) Node, University of Luxembourg, Campus Belval, House of Biomedicine II, 6 avenue du Swing, L-4367 Belvaux, Luxembourg
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Reinhard Schneider
Burkhard Rost
1TUM (Technical University of Munich) Dept Informatics, Bioinformatics & Comp Biology - i12, Boltzmannstr 3, 85748 Garching/Munich, Germany
21Inst for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748 Garching/Munich, Germany
22TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Burkhard Rost
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Since 1992 PredictProtein (https://predictprotein.org) is a one-stop online resource for protein sequence analysis with its main site hosted at the Luxembourg Centre for Systems Biomedicine (LCSB) and queried monthly by over 3,000 users in 2020. 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; 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.

Availability Freely accessible webserver PredictProtein.org; Source and docker images: github.com/rostlab

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
Back to top
PreviousNext
Posted February 24, 2021.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
PredictProtein – Predicting Protein Structure and Function for 29 Years
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
PredictProtein – Predicting Protein Structure and Function for 29 Years
Michael Bernhofer, Christian Dallago, Tim Karl, Venkata Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, Laszlo Kajan, Sean O’Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost
bioRxiv 2021.02.23.432527; doi: https://doi.org/10.1101/2021.02.23.432527
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
PredictProtein – Predicting Protein Structure and Function for 29 Years
Michael Bernhofer, Christian Dallago, Tim Karl, Venkata Satagopam, Michael Heinzinger, Maria Littmann, Tobias Olenyi, Jiajun Qiu, Konstantin Schütze, Guy Yachdav, Haim Ashkenazy, Nir Ben-Tal, Yana Bromberg, Tatyana Goldberg, Laszlo Kajan, Sean O’Donoghue, Chris Sander, Andrea Schafferhans, Avner Schlessinger, Gerrit Vriend, Milot Mirdita, Piotr Gawron, Wei Gu, Yohan Jarosz, Christophe Trefois, Martin Steinegger, Reinhard Schneider, Burkhard Rost
bioRxiv 2021.02.23.432527; doi: https://doi.org/10.1101/2021.02.23.432527

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Bioinformatics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3479)
  • Biochemistry (7318)
  • Bioengineering (5296)
  • Bioinformatics (20196)
  • Biophysics (9976)
  • Cancer Biology (7701)
  • Cell Biology (11249)
  • Clinical Trials (138)
  • Developmental Biology (6417)
  • Ecology (9915)
  • Epidemiology (2065)
  • Evolutionary Biology (13276)
  • Genetics (9352)
  • Genomics (12551)
  • Immunology (7673)
  • Microbiology (18937)
  • Molecular Biology (7417)
  • Neuroscience (40887)
  • Paleontology (298)
  • Pathology (1226)
  • Pharmacology and Toxicology (2125)
  • Physiology (3140)
  • Plant Biology (6837)
  • Scientific Communication and Education (1270)
  • Synthetic Biology (1891)
  • Systems Biology (5296)
  • Zoology (1084)