Marco Punta

Publication Activity (10 Years)

Years Active: 2005-2022
Publications (10 Years): 7

Top Topics

Amino Acid Composition

Protein Families

Top Venues

Nucleic Acids Res.

Database J. Biol. Databases Curation

Briefings Bioinform.

Publications

Elena Tea Russo, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio
DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets. PLoS Comput. Biol. 18 (10) (2022)
Elena Tea Russo, Alessandro Laio, Marco Punta
Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. BMC Bioinform. 22 (1) (2021)
Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John G. Tate, Alex Bateman
The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44 (Database-Issue) (2016)
Tony E. Lewis, Ian Sillitoe, Antonina Andreeva, Tom L. Blundell, Daniel W. A. Buchan, Cyrus Chothia, Domenico Cozzetto, Jose M. Dana, Ioannis Filippis, Julian Gough, David T. Jones, Lawrence A. Kelley, Gerard J. Kleywegt, Federico Minneci, Jaina Mistry, Alexey G. Murzin, Bernardo Ochoa-Montaño, Matt E. Oates, Marco Punta, Owen J. L. Rackham, Jonathan Stahlhacke, Michael J. E. Sternberg, Sameer Velankar, Christine A. Orengo
Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Res. 43 (Database-Issue) (2015)
Padmaja Natarajan, Marco Punta, Abhinav Kumar, Andrew P. Yeh, Adam Godzik, L. Aravind
Structure and sequence analyses of Bacteroides proteins BVU_4064 and BF1687 reveal presence of two novel predominantly-beta domains, predicted to be involved in lipid and cell surface interactions. BMC Bioinform. 16 (2015)
Zachary Chiang, Åke Västermark, Marco Punta, Penelope Coggill, Jaina Mistry, Robert D. Finn, Milton H. Saier Jr.
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. Briefings Bioinform. 16 (5) (2015)
Alex L. Mitchell, Hsin-Yu Chang, Louise C. Daugherty, Matthew Fraser, Sarah Hunter, Rodrigo Lopez, Craig McAnulla, Conor McMenamin, Gift Nuka, Sebastien Pesseat, Amaia Sangrador-Vegas, Maxim Scheremetjew, Claudia Rato, Siew-Yit Yong, Alex Bateman, Marco Punta, Teresa K. Attwood, Christian J. A. Sigrist, Nicole Redaschi, Catherine Rivoire, Ioannis Xenarios, Daniel Kahn, Dominique Guyot, Peer Bork, Ivica Letunic, Julian Gough, Matt E. Oates, Daniel H. Haft, Hongzhan Huang, Darren A. Natale, Cathy H. Wu, Christine A. Orengo, Ian Sillitoe, Huaiyu Mi, Paul D. Thomas, Robert D. Finn
The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Res. 43 (Database-Issue) (2015)
Robert D. Finn, Alex Bateman, Jody Clements, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Andreas Heger, Kirstie Hetherington, Liisa Holm, Jaina Mistry, Erik L. L. Sonnhammer, John G. Tate, Marco Punta
Pfam: the protein families database. Nucleic Acids Res. 42 (Database-Issue) (2014)
Christine B. Trame, Yuanyuan Chang, Herbert L. Axelrod, Ruth Y. Eberhardt, Penelope Coggill, Marco Punta, Neil D. Rawlings
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. BMC Bioinform. 15 (2014)
Guy Yachdav, Edda Kloppmann, László Kaján, Maximilian Hecht, Tatyana Goldberg, Tobias Hamp, Peter Hönigschmid, Andrea Schafferhans, Manfred Roos, Michael Bernhofer, Lothar Richter, Haim Ashkenazy, Marco Punta, Avner Schlessinger, Yana Bromberg, Reinhard Schneider, Gerrit Vriend, Chris Sander, Nir Ben-Tal, Burkhard Rost
PredictProtein - an open resource for online prediction of protein structural and functional features. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta
The challenge of increasing Pfam coverage of the human proteome. Database J. Biol. Databases Curation 2013 (2013)
Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta
The challenge of increasing Pfam coverage of the human proteome. Database J. Biol. Databases Curation 2013 (2013)
William C. Hwang, Constantina Bakolitsa, Marco Punta, Penelope Coggill, Alex Bateman, Herbert L. Axelrod, Neil D. Rawlings, Mayya Sedova, Scott N. Peterson, Ruth Y. Eberhardt, L. Aravind, Jaime Pascual, Adam Godzik
LUD, a new protein domain associated with lactate utilization. BMC Bioinform. 14 (2013)
Sarah Hunter, Philip Jones, Alex L. Mitchell, Rolf Apweiler, Teresa K. Attwood, Alex Bateman, Thomas Bernard, David Binns, Peer Bork, Sarah W. Burge, Edouard De Castro, Penny C. Coggill, Matthew Corbett, Ujjwal Das, Louise C. Daugherty, Lauranne Duquenne, Robert D. Finn, Matthew Fraser, Julian Gough, Daniel H. Haft, Nicolas Hulo, Daniel Kahn, Elizabeth Kelly, Ivica Letunic, David Lonsdale, Rodrigo Lopez, Martin Madera, John Maslen, Craig McAnulla, Jennifer McDowall, Conor McMenamin, Huaiyu Mi, Prudence Mutowo-Meullenet, Nicola J. Mulder, Darren A. Natale, Christine A. Orengo, Sebastien Pesseat, Marco Punta, Antony F. Quinn, Catherine Rivoire, Amaia Sangrador-Vegas, Jeremy D. Selengut, Christian J. A. Sigrist, Maxim Scheremetjew, John G. Tate, Manjulapramila Thimmajanarthanan, Paul D. Thomas, Cathy H. Wu, Corin Yeats, Siew-Yit Yong
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 40 (Database-Issue) (2012)
Marco Lippi, Andrea Passerini, Marco Punta, Paolo Frasconi
Metal Binding in Proteins: Machine Learning Complements X-Ray Absorption Spectroscopy. ECML/PKDD (2) (2012)
Marco Punta, Penny C. Coggill, Ruth Y. Eberhardt, Jaina Mistry, John G. Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements, Andreas Heger, Liisa Holm, Erik L. L. Sonnhammer, Sean R. Eddy, Alex Bateman, Robert D. Finn
The Pfam protein families database. Nucleic Acids Res. 40 (Database-Issue) (2012)
Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Jesus Martin, Claire O'Donovan, Alex Bateman
AntiFam: a tool to help identify spurious ORFs in protein annotation. Database J. Biol. Databases Curation 2012 (2012)
Marco Punta, Yanay Ofran
The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function. PLoS Comput. Biol. 4 (10) (2008)
Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann
Session Introduction. Pacific Symposium on Biocomputing (2008)
Marco Lippi, Andrea Passerini, Marco Punta, Burkhard Rost, Paolo Frasconi
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. Bioinform. 24 (18) (2008)
Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
Session Introduction. Pacific Symposium on Biocomputing (2007)
Avner Schlessinger, Marco Punta, Burkhard Rost
Natively unstructured regions in proteins identified from contact predictions. Bioinform. 23 (18) (2007)
Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
Session Introduction. Pacific Symposium on Biocomputing (2006)
Marco Punta, Burkhard Rost
PROFcon: novel prediction of long-range contacts. Bioinform. 21 (13) (2005)