Search Results - "Silvio, Tosatto"

The RING 2.0 web server for high quality residue interaction networks by Piovesan, Damiano, Minervini, Giovanni, Tosatto, Silvio C E

“…Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions…”
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PASTA 2.0: an improved server for protein aggregation prediction by Walsh, Ian, Seno, Flavio, Tosatto, Silvio C E, Trovato, Antonio

“…The formation of amyloid aggregates upon protein misfolding is related to several devastating degenerative diseases. The propensities of different protein…”
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The Pfam protein families database in 2019 by El-Gebali, Sara, Mistry, Jaina, Bateman, Alex, Eddy, Sean R, Luciani, Aurélien, Potter, Simon C, Qureshi, Matloob, Richardson, Lorna J, Salazar, Gustavo A, Smart, Alfredo, Sonnhammer, Erik L L, Hirsh, Layla, Paladin, Lisanna, Piovesan, Damiano, Tosatto, Silvio C E, Finn, Robert D

“…Abstract The last few years have witnessed significant changes in Pfam (https://pfam.xfam.org). The number of families has grown substantially to a total of…”
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FuzDrop on AlphaFold: visualizing the sequence-dependent propensity of liquid–liquid phase separation and aggregation of proteins by Hatos, Andras, Tosatto, Silvio C E, Vendruscolo, Michele, Fuxreiter, Monika

“…Abstract Many proteins perform their functions within membraneless organelles, where they form a liquid-like condensed state, also known as droplet state. The…”
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MobiDB: intrinsically disordered proteins in 2021 by Piovesan, Damiano, Necci, Marco, Escobedo, Nahuel, Monzon, Alexander Miguel, Hatos, András, Mičetić, Ivan, Quaglia, Federica, Paladin, Lisanna, Ramasamy, Pathmanaban, Dosztányi, Zsuzsanna, Vranken, Wim F, Davey, Norman E, Parisi, Gustavo, Fuxreiter, Monika, Tosatto, Silvio C E

“…Abstract The MobiDB database (URL: https://mobidb.org/) provides predictions and annotations for intrinsically disordered proteins. Here, we report recent…”
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Pfam: The protein families database in 2021 by Mistry, Jaina, Chuguransky, Sara, Williams, Lowri, Qureshi, Matloob, Salazar, Gustavo A, Sonnhammer, Erik L L, Tosatto, Silvio C E, Paladin, Lisanna, Raj, Shriya, Richardson, Lorna J, Finn, Robert D, Bateman, Alex

“…Abstract The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this…”
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MobiDB-lite: Fast and highly specific consensus prediction of intrinsic disorder in proteins by Necci, Marco, Piovesan, Damiano, Dosztányi, Zsuzsanna, Tosatto, Silvio C E

“…Intrinsic disorder (ID) is established as an important feature of protein sequences. Its use in proteome annotation is however hampered by the availability of…”
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InterPro in 2022 by Paysan-Lafosse, Typhaine, Blum, Matthias, Chuguransky, Sara, Grego, Tiago, Pinto, Beatriz Lázaro, Salazar, Gustavo A, Bileschi, Maxwell L, Bork, Peer, Bridge, Alan, Colwell, Lucy, Gough, Julian, Haft, Daniel H, Letunić, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, Sigrist, Christian J A, Sillitoe, Ian, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex

“…The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally…”
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Intrinsic protein disorder and conditional folding in AlphaFoldDB by Piovesan, Damiano, Monzon, Alexander Miguel, Tosatto, Silvio C. E.

“…Intrinsically disordered regions (IDRs) defying the traditional protein structure–function paradigm have been difficult to analyze. The availability of…”
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InterPro in 2017-beyond protein family and domain annotations by Finn, Robert D, Attwood, Teresa K, Babbitt, Patricia C, Bateman, Alex, Bork, Peer, Bridge, Alan J, Chang, Hsin-Yu, Dosztányi, Zsuzsanna, El-Gebali, Sara, Fraser, Matthew, Gough, Julian, Haft, David, Holliday, Gemma L, Huang, Hongzhan, Huang, Xiaosong, Letunic, Ivica, Lopez, Rodrigo, Lu, Shennan, Marchler-Bauer, Aron, Mi, Huaiyu, Mistry, Jaina, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine A, Park, Youngmi, Pesseat, Sebastien, Piovesan, Damiano, Potter, Simon C, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna, Rivoire, Catherine, Sangrador-Vegas, Amaia, Sigrist, Christian, Sillitoe, Ian, Smithers, Ben, Squizzato, Silvano, Sutton, Granger, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Xenarios, Ioannis, Yeh, Lai-Su, Young, Siew-Yit, Mitchell, Alex L

“…InterPro (http://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of…”
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SARS‐CoV‐2 variants preferentially emerge at intrinsically disordered protein sites helping immune evasion by Quaglia, Federica, Salladini, Edoardo, Carraro, Marco, Minervini, Giovanni, Tosatto, Silvio C.E., Le Mercier, Philippe

“…The SARS‐CoV‐2 pandemic is maintained by the emergence of successive variants, highlighting the flexibility of the protein sequences of the virus. We show that…”
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InterPro in 2019: improving coverage, classification and access to protein sequence annotations by Mitchell, Alex L, Attwood, Teresa K, Babbitt, Patricia C, Blum, Matthias, Bork, Peer, Bridge, Alan, Brown, Shoshana D, Chang, Hsin-Yu, El-Gebali, Sara, Fraser, Matthew I, Gough, Julian, Haft, David R, Huang, Hongzhan, Letunic, Ivica, Lopez, Rodrigo, Luciani, Aurélien, Madeira, Fabio, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Necci, Marco, Nuka, Gift, Orengo, Christine, Pandurangan, Arun P, Paysan-Lafosse, Typhaine, Pesseat, Sebastien, Potter, Simon C, Qureshi, Matloob A, Rawlings, Neil D, Redaschi, Nicole, Richardson, Lorna J, Rivoire, Catherine, Salazar, Gustavo A, Sangrador-Vegas, Amaia, Sigrist, Christian J A, Sillitoe, Ian, Sutton, Granger G, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Yong, Siew-Yit, Finn, Robert D

“…Abstract The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important…”
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MobiDB: 10 years of intrinsically disordered proteins by Piovesan, Damiano, Del Conte, Alessio, Clementel, Damiano, Monzon, Alexander Miguel, Bevilacqua, Martina, Aspromonte, Maria Cristina, Iserte, Javier A, Orti, Fernando E, Marino-Buslje, Cristina, Tosatto, Silvio C E

“…The MobiDB database (URL: https://mobidb.org/) is a knowledge base of intrinsically disordered proteins. MobiDB aggregates disorder annotations derived from…”
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ESpritz: accurate and fast prediction of protein disorder by Walsh, Ian, Martin, Alberto J. M., Di Domenico, Tomàs, Tosatto, Silvio C. E.

“…Motivation: Intrinsically disordered regions are key for the function of numerous proteins, and the scant available experimental annotations suggest the…”
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FELLS: fast estimator of latent local structure by Piovesan, Damiano, Walsh, Ian, Minervini, Giovanni, Tosatto, Silvio C E

“…The behavior of a protein is encoded in its sequence, which can be used to predict distinct features such as secondary structure, intrinsic disorder or…”
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The InterPro protein families and domains database: 20 years on by Blum, Matthias, Chang, Hsin-Yu, Chuguransky, Sara, Grego, Tiago, Kandasaamy, Swaathi, Mitchell, Alex, Nuka, Gift, Paysan-Lafosse, Typhaine, Qureshi, Matloob, Raj, Shriya, Richardson, Lorna, Salazar, Gustavo A, Williams, Lowri, Bork, Peer, Bridge, Alan, Gough, Julian, Haft, Daniel H, Letunic, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Necci, Marco, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, Sigrist, Christian J A, Sillitoe, Ian, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex, Finn, Robert D

“…Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies…”
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SODA: prediction of protein solubility from disorder and aggregation propensity by Paladin, Lisanna, Piovesan, Damiano, Tosatto, Silvio C E

“…Solubility is an important, albeit not well understood, feature determining protein behavior. It is of paramount importance in protein engineering, where…”
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FuzDB: a new phase in understanding fuzzy interactions by Hatos, Andras, Monzon, Alexander Miguel, Tosatto, Silvio C E, Piovesan, Damiano, Fuxreiter, Monika

“…Abstract Fuzzy interactions are specific, variable contacts between proteins and other biomolecules (proteins, DNA, RNA, small molecules) formed in accord to…”
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MobiDB: a comprehensive database of intrinsic protein disorder annotations by DI DOMENICO, Tomás, WALSH, Ian, MARTIN, Alberto J. M, TOSATTO, Silvio C. E

“…Disordered protein regions are key to the function of numerous processes within an organism and to the determination of a protein's biological role. The most…”
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DOME: recommendations for supervised machine learning validation in biology by Walsh, Ian, Fishman, Dmytro, Garcia-Gasulla, Dario, Titma, Tiina, Pollastri, Gianluca, Harrow, Jennifer, Psomopoulos, Fotis E., Tosatto, Silvio C. E.

“…DOME is a set of community-wide recommendations for reporting supervised machine learning–based analyses applied to biological studies. Broad adoption of these…”
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