Marco Punta

25 papers Misc 3Journal 20Unranked 1
YearRankTypeTitle / Venue / Authors
2022 J jnl
DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets.
PLoS Comput. Biol.
Elena Tea Russo, Federico Barone, Alex Bateman, Stefano Cozzini, Marco Punta, Alessandro Laio
2021 J jnl
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.
Elena Tea Russo, Alessandro Laio, Marco Punta
2016 J jnl
The Pfam protein families database: towards a more sustainable future.
Nucleic Acids Res.
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
2015 J jnl
Genome3D: exploiting structure to help users understand their sequences.
Nucleic Acids Res.
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
2015 J jnl
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.
Padmaja Natarajan, Marco Punta, Abhinav Kumar, Andrew P. Yeh, Adam Godzik, L. Aravind
2015 J jnl
The InterPro protein families database: the classification resource after 15 years.
Nucleic Acids Res.
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
2015 J jnl
The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.
Briefings Bioinform.
Zachary Chiang, Åke Västermark, Marco Punta, Penelope Coggill, Jaina Mistry, Robert D. Finn, Milton H. Saier Jr.
2014 J jnl
New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.
BMC Bioinform.
Christine B. Trame, Yuanyuan Chang, Herbert L. Axelrod, Ruth Y. Eberhardt, Penelope Coggill, Marco Punta, Neil D. Rawlings
2014 J jnl
Pfam: the protein families database.
Nucleic Acids Res.
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
2014 J jnl
PredictProtein - an open resource for online prediction of protein structural and functional features.
Nucleic Acids Res.
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
2013 J jnl
LUD, a new protein domain associated with lactate utilization.
BMC Bioinform.
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
2013 J jnl
The challenge of increasing Pfam coverage of the human proteome.
Database J. Biol. Databases Curation
Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta
2013 J jnl
The challenge of increasing Pfam coverage of the human proteome.
Database J. Biol. Databases Curation
Jaina Mistry, Penny C. Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, Marco Punta
2012 J jnl
AntiFam: a tool to help identify spurious ORFs in protein annotation.
Database J. Biol. Databases Curation
Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Jesus Martin, Claire O'Donovan, Alex Bateman
2012 J jnl
InterPro in 2011: new developments in the family and domain prediction database.
Nucleic Acids Res.
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
2012 — conf
Metal Binding in Proteins: Machine Learning Complements X-Ray Absorption Spectroscopy.
ECML/PKDD (2)
Marco Lippi, Andrea Passerini, Marco Punta, Paolo Frasconi
2012 J jnl
The Pfam protein families database.
Nucleic Acids Res.
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
2009 — ch.
Neural Networks Predict Protein Structure and Function.
Artificial Neural Networks
Marco Punta, Burkhard Rost
2008 J jnl
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.
Bioinform.
Marco Lippi, Andrea Passerini, Marco Punta, Burkhard Rost, Paolo Frasconi
2008 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Yves A. Lussier, Younghee Lee, Predrag Radivojac, Yanay Ofran, Marco Punta, Atul J. Butte, Maricel G. Kann
2008 J jnl
The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function.
PLoS Comput. Biol.
Marco Punta, Yanay Ofran
2007 J jnl
Natively unstructured regions in proteins identified from contact predictions.
Bioinform.
Avner Schlessinger, Marco Punta, Burkhard Rost
2007 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
2006 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
Maricel G. Kann, Yanay Ofran, Marco Punta, Predrag Radivojac
2005 J jnl
PROFcon: novel prediction of long-range contacts.
Bioinform.
Marco Punta, Burkhard Rost