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Driving the functional characterization of intrinsically disordered proteins

Deliverables

Software to discriminate different types of disorder based on amino acid propensities and other features

Software to discriminate different types of disorder based on amino acid propensities and other features.

Software package for the automatic extraction of PED entry data from protein ensembles

Software package for the automatic extraction of PED entry data from protein ensembles.

New version of the Mobi software

New version of the Mobi software.

Software for the identification of homologous IDR clusters from sequence databases

Software for the identification of homologous IDR clusters from sequence databases.

A software tool for the automatic extraction of IDR relevant information from literature

A software tool for the automatic extraction of IDR relevant information from literature.

Software for automatic detection of IDRs and linear motifs from protein structures

Software pipeline for the automatic extraction of X-ray derived IDR information (missing electron densities), linear motifs and consensus generation.

Symposia Period 1

Twice in Europe: Administrative visit. ESR symposium. Scientific symposium. Hackathon. Train-the-trainers. Transferable skills symposium. Career development. SB and AB meeting. Twice in Argentina: ESR Symposium. Training bootcamp. SB meeting. Public outreach activities.

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Publications

Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins

Author(s): Marco Necci, Damiano Piovesan, Silvio C E Tosatto
Published in: Database, Issue 2018, 2018, ISSN 1758-0463
DOI: 10.1093/database/bay127

Disentangling the complexity of low complexity proteins

Author(s): Pablo Mier, Lisanna Paladin, Stella Tamana, Sophia Petrosian, Borbála Hajdu-Soltész, Annika Urbanek, Aleksandra Gruca, Dariusz Plewczynski, Marcin Grynberg, Pau Bernadó, Zoltán Gáspári, Christos A Ouzounis, Vasilis J Promponas, Andrey V Kajava, John M Hancock, Silvio C E Tosatto, Zsuzsanna Dosztanyi, Miguel A Andrade-Navarro
Published in: Briefings in Bioinformatics, Issue 2019, 2019, ISSN 1467-5463
DOI: 10.1093/bib/bbz007

Ensembles from Ordered and Disordered Proteins Reveal Similar Structural Constraints during Evolution

Author(s): Julia Marchetti, Alexander Miguel Monzon, Silvio C.E. Tosatto, Gustavo Parisi, María Silvina Fornasari
Published in: Journal of Molecular Biology, Issue 431/6, 2019, Page(s) 1298-1307, ISSN 0022-2836
DOI: 10.1016/j.jmb.2019.01.031

INGA 2.0: improving protein function prediction for the dark proteome

Author(s): Damiano Piovesan, Silvio C E Tosatto
Published in: Nucleic Acids Research, Issue 47/W1, 2019, Page(s) W373-W378, ISSN 0305-1048
DOI: 10.1093/nar/gkz375

DisProt: intrinsic protein disorder annotation in 2020

Author(s): András Hatos, Borbála Hajdu-Soltész, Alexander M Monzon, Nicolas Palopoli, Lucía Álvarez, Burcu Aykac-Fas, Claudio Bassot, Guillermo I Benítez, Martina Bevilacqua, Anastasia Chasapi, Lucia Chemes, Norman E Davey, Radoslav Davidović, A Keith Dunker, Arne Elofsson, Julien Gobeill, Nicolás S González Foutel, Govindarajan Sudha, Mainak Guharoy, Tamas Horvath, Valentin Iglesias, Andrey V Kaj
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
DOI: 10.1093/nar/gkz975

PhaSePro: the database of proteins driving liquid–liquid phase separation

Author(s): Bálint Mészáros, Gábor Erdős, Beáta Szabó, Éva Schád, Ágnes Tantos, Rawan Abukhairan, Tamás Horváth, Nikoletta Murvai, Orsolya P Kovács, Márton Kovács, Silvio C E Tosatto, Péter Tompa, Zsuzsanna Dosztányi, Rita Pancsa
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
DOI: 10.1093/nar/gkz848

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Author(s): Naihui Zhou, Yuxiang Jiang, Timothy R. Bergquist, Alexandra J. Lee, Balint Z. Kacsoh, Alex W. Crocker, Kimberley A. Lewis, George Georghiou, Huy N. Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S. Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L. Hurto, Peter L. Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M. Fernández, Branislava Ge
Published in: Genome Biology, Issue 20/1, 2019, ISSN 1474-760X
DOI: 10.1186/s13059-019-1835-8