PROFcon: novel prediction of long-range contacts. - Marco Punta; Burkhard Rost (Bioinform., 2005)

Session Introduction. - Maricel G. Kann; Yanay Ofran; Marco Punta; Predrag Radivojac (Pacific Symposium on Biocomputing, 2006)

Natively unstructured regions in proteins identified from contact predictions. - Avner Schlessinger; Marco Punta; Burkhard Rost (Bioinform., 2007)

Session Introduction. - Yves A. Lussier; Younghee Lee; Predrag Radivojac; Yanay Ofran; Marco Punta; Atul J. Butte; Maricel G. Kann (Pacific Symposium on Biocomputing, 2008)

MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence. - Marco Lippi 001; Andrea Passerini; Marco Punta; Burkhard Rost; Paolo Frasconi (Bioinform., 2008)

The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function. - Marco Punta; Yanay Ofran (PLoS Comput. Biol., 2008)

Neural Networks Predict Protein Structure and Function. - Marco Punta; Burkhard Rost (Artificial Neural Networks, 2009)

Metal Binding in Proteins: Machine Learning Complements X-Ray Absorption Spectroscopy. - Marco Lippi 001; Andrea Passerini; Marco Punta; Paolo Frasconi (ECML/PKDD (2), 2012)

AntiFam: a tool to help identify spurious ORFs in protein annotation. - Ruth Y. Eberhardt; Daniel H. Haft; Marco Punta; Maria Jesus Martin; Claire O'Donovan; Alex Bateman (Database J. Biol. Databases Curation, 2012)

InterPro in 2011: new developments in the family and domain prediction database. - 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; et al. (Nucleic Acids Res., 2012)

The Pfam protein families database. - 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; et al. (Nucleic Acids Res., 2012)

The challenge of increasing Pfam coverage of the human proteome. - Jaina Mistry; Penny C. Coggill; Ruth Y. Eberhardt; Antonio Deiana; Andrea Giansanti; Robert D. Finn; Alex Bateman; Marco Punta (Database J. Biol. Databases Curation, 2013)

LUD, a new protein domain associated with lactate utilization. - 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; et al. (BMC Bioinform., 2013)

New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily. - Christine B. Trame; Yuanyuan Chang; Herbert L. Axelrod; Ruth Y. Eberhardt; Penelope Coggill; Marco Punta; Neil D. Rawlings (BMC Bioinform., 2014)

Pfam: the protein families database. - 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; et al. (Nucleic Acids Res., 2014)

PredictProtein - an open resource for online prediction of protein structural and functional features. - Guy Yachdav; Edda Kloppmann; László Kaján; Maximilian Hecht; Tatyana Goldberg; Tobias Hamp; Peter Hönigschmid; Andrea Schafferhans; Manfred Roos; Michael Bernhofer; Lothar Richter; Haim Ashkenazy; et al. (Nucleic Acids Res., 2014)

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam. - Zachary Chiang; Åke Västermark; Marco Punta; Penelope Coggill; Jaina Mistry; Robert D. Finn; Milton H. Saier Jr. (Briefings Bioinform., 2015)

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. - Padmaja Natarajan; Marco Punta; Abhinav Kumar; Andrew P. Yeh; Adam Godzik; L. Aravind (BMC Bioinform., 2015)

Genome3D: exploiting structure to help users understand their sequences. - 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; et al. (Nucleic Acids Res., 2015)

The InterPro protein families database: the classification resource after 15 years. - 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; et al. (Nucleic Acids Res., 2015)

The Pfam protein families database: towards a more sustainable future. - 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; et al. (Nucleic Acids Res., 2016)

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation. - Elena Tea Russo; Alessandro Laio; Marco Punta (BMC Bioinform., 2021)

DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets. - Elena Tea Russo; Federico Barone; Alex Bateman; Stefano Cozzini; Marco Punta; Alessandro Laio (PLoS Comput. Biol., 2022)