Works by Punta, Marco

Results: 41

The complexity, challenges and benefits of comparing two transporter classification systems in TCDB and Pfam.

Published in:

Briefings in Bioinformatics, 2015, v. 16, n. 5, p. 865, doi. 10.1093/bib/bbu053

By:

Chiang, Zachary;
Vastermark, Ake;
Punta, Marco;
Coggill, Penelope C.;
Mistry, Jaina;
Finn, Robert D.;
Saier Jr., Milton H.

Publication type:

Article

Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity.

Published in:

Nature Communications, 2018, v. 9, n. 1, p. 1, doi. 10.1038/s41467-018-06130-3

By:

Heindl, Andreas;
Khan, Adnan Mujahid;
Rodrigues, Daniel Nava;
Eason, Katherine;
Sadanandam, Anguraj;
Orbegoso, Cecilia;
Punta, Marco;
Sottoriva, Andrea;
Lise, Stefano;
Banerjee, Susana;
Yuan, Yinyin

Publication type:

Article

Crystal structure of a phosphorylation-coupled saccharide transporter.

Published in:

Nature, 2011, v. 473, n. 7345, p. 50, doi. 10.1038/nature09939

By:

Yu Cao;
Xiangshu Jin;
Levin, Elena J.;
Hua Huang;
Yinong Zong;
Quick, Matthias;
Jun Weng;
Yaping Pan;
Love, James;
Punta, Marco;
Rost, Burkhard;
Hendrickson, Wayne A.;
Javitch, Jonathan A.;
Rajashankar, Kanagalaghatta R.;
Ming Zhou

Publication type:

Article

Crystal structure of a potassium ion transporter, TrkH.

Published in:

Nature, 2011, v. 471, n. 7338, p. 336, doi. 10.1038/nature09731

By:

Yu Cao;
Xiangshu Jin;
Hua Huang;
Derebe, Mehabaw Getahun;
Levin, Elena J.;
Kabaleeswaran, Venkataraman;
Pan, Yaping;
Punta, Marco;
Love, James;
Jun Weng;
Quick, Matthias;
Sheng Ye;
Kloss, Brian;
Bruni, Renato;
Martinez-Hackert, Erik;
Hendrickson, Wayne A.;
Rost, Burkhard;
Javitch, Jonathan A.;
Rajashankar, Kanagalaghatta R.;
Youxing Jiang

Publication type:

Article

Homologue structure of the SLAC1 anion channel for closing stomata in leaves.

Published in:

Nature, 2010, v. 467, n. 7319, p. 1074, doi. 10.1038/nature09487

By:

Yu-hang Chen;
Lei Hu;
Punta, Marco;
Bruni, Renato;
Hillerich, Brandan;
Kloss, Brian;
Rost, Burkhard;
Love, James;
Siegelbaum, Steven A.;
Hendrickson, Wayne A.

Publication type:

Article

Protein family annotation for the Unified Human Gastrointestinal Proteome by DPCfam clustering.

Published in:

Scientific Data, 2024, v. 11, n. 1, p. 1, doi. 10.1038/s41597-024-03131-4

By:

Barone, Federico;
Russo, Elena Tea;
Villegas Garcia, Edith Natalia;
Punta, Marco;
Cozzini, Stefano;
Ansuini, Alessio;
Cazzaniga, Alberto

Publication type:

Article

Phase II trial of hypomethylating agent combined with nivolumab for acute myeloid leukaemia relapse after allogeneic haematopoietic cell transplantation—Immune signature correlates with response.

Published in:

British Journal of Haematology, 2023, v. 203, n. 2, p. 264, doi. 10.1111/bjh.19007

By:

Apostolova, Petya;
Kreutmair, Stefanie;
Toffalori, Cristina;
Punta, Marco;
Unger, Susanne;
Burk, Ann‐Cathrin;
Wehr, Claudia;
Maas‐Bauer, Kristina;
Melchinger, Wolfgang;
Haring, Eileen;
Hoefflin, Rouven;
Shoumariyeh, Khalid;
Hupfer, Valerie;
Lauer, Eliza Maria;
Duquesne, Sandra;
Lowinus, Theresa;
Gonzalo Núñez, Nicolás;
Alberti, Chiara;
da Costa Pereira, Sara;
Merten, Carla Helena

Publication type:

Article

Density Peak clustering of protein sequences associated to a Pfam clan reveals clear similarities and interesting differences with respect to manual family annotation.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04013-x

By:

Russo, Elena Tea;
Laio, Alessandro;
Punta, Marco

Publication type:

Article

MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence.

Published in:

Bioinformatics, 2008, v. 24, n. 18, p. 2094, doi. 10.1093/bioinformatics/btn371

By:

Marco Lippi;
Andrea Passerini;
Marco Punta;
Burkhard Rost;
Paolo Frasconi

Publication type:

Article

Natively unstructured regions in proteins identified from contact predictions.

Published in:

Bioinformatics, 2007, v. 23, n. 18, p. 2376, doi. 10.1093/bioinformatics/btm349

By:

Avner Schlessinger;
Marco Punta;
Burkhard Rost

Publication type:

Article

PROFcon: novel prediction of long-range contacts.

Published in:

Bioinformatics, 2005, v. 21, n. 13, p. 2960, doi. 10.1093/bioinformatics/bti454

By:

Marco Punta;
Burkhard Rost

Publication type:

Article

Impact of predicted HLA class I immunopeptidome on viral reservoir in a cohort of people living with HIV in Italy.

Published in:

HLA: Immune Response Genetics, 2024, v. 103, n. 1, p. 1, doi. 10.1111/tan.15298

By:

Rovatti, Pier Edoardo;
Muccini, Camilla;
Punta, Marco;
Galli, Laura;
Mainardi, Ilaria;
Ponta, Giacomo;
Vago, Luca Aldo Edoardo;
Castagna, Antonella

Publication type:

Article

T-cell receptor determinants of response to chemoradiation in locally-advanced HPV16-driven malignancies.

Published in:

Frontiers in Oncology, 2024, p. 1, doi. 10.3389/fonc.2023.1296948

By:

Nenclares, Pablo;
Larkeryd, Adrian;
Manodoro, Floriana;
Lee, Jen Y.;
Lalondrelle, Susan;
Gilbert, Duncan C.;
Punta, Marco;
O'Leary, Ben;
Rullan, Antonio;
Sadanandam, Anguraj;
Chain, Benny;
Melcher, Alan;
Harrington, Kevin J.;
Bhide, Shreerang A.

Publication type:

Article

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.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 1, doi. 10.1186/s12859-014-0434-7

By:

Natarajan, Padmaja;
Punta, Marco;
Kumar, Abhinav;
Yeh, Andrew P.;
Godzik, Adam;
Aravind, L.

Publication type:

Article

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.

Published in:

BMC Bioinformatics, 2015, v. 16, n. 1, p. 225, doi. 10.1186/s12859-014-0434-7

By:

Natarajan, Padmaja;
Punta, Marco;
Kumar, Abhinav;
Yeh, Andrew P.;
Godzik, Adam;
Aravind, L.

Publication type:

Article

New mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.

Published in:

BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-1

By:

Trame, Christine B.;
Yuanyuan Chang;
Axelrod, Herbert L.;
Eberhardt, Ruth Y.;
Coggill, Penelope;
Punta, Marco;
Rawlings, Neil D.

Publication type:

Article

LUD, a new protein domain associated with lactate utilization.

Published in:

BMC Bioinformatics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2105-14-341

By:

Hwang, William C.;
Bakolitsa, Constantina;
Punta, Marco;
Coggill, Penelope C.;
Bateman, Alex;
Axelrod, Herbert L.;
Rawlings, Neil D.;
Sedova, Mayya;
Peterson, Scott N.;
Eberhardt, Ruth Y.;
Aravind, L.;
Pascual, Jaime;
Godzik, Adam

Publication type:

Article

The Pfam protein families database: towards a more sustainable future.

Published in:

Nucleic Acids Research, 2016, v. 44, p. D279, doi. 10.1093/nar/gkv1344

By:

Finn, Robert D.;
Coggill, Penelope;
Eberhardt, Ruth Y.;
Eddy, Sean R.;
Mistry, Jaina;
Mitchell, Alex L.;
Potter, Simon C.;
Punta, Marco;
Qureshi, Matloob;
Sangrador-Vegas, Amaia;
Salazar, Gustavo A.;
Tate, John;
Bateman, Alex

Publication type:

Article

Genome3D: exploiting structure to help users understand their sequences.

Published in:

Nucleic Acids Research, 2015, v. 43, n. D1, p. D382, doi. 10.1093/nar/gku973

By:

Lewis, Tony E.;
Sillitoe, Ian;
Andreeva, Antonina;
Blundell, Tom L.;
Buchan, Daniel W.A.;
Chothia, Cyrus;
Cozzetto, Domenico;
Dana, José M.;
Filippis, Ioannis;
Gough, Julian;
Jones, David T.;
Kelley, Lawrence A.;
Kleywegt, Gerard J.;
Minneci, Federico;
Mistry, Jaina;
Murzin, Alexey G.;
Ochoa-Montaño, Bernardo;
Oates, Matt E.;
Punta, Marco;
Rackham, Owen J.L.

Publication type:

Article

The InterPro protein families database: the classification resource after 15 years.

Published in:

Nucleic Acids Research, 2015, v. 43, n. D1, p. D213, doi. 10.1093/nar/gku1243

By:

Mitchell, Alex;
Chang, Hsin-Yu;
Daugherty, Louise;
Fraser, Matthew;
Hunter, Sarah;
Lopez, Rodrigo;
McAnulla, Craig;
McMenamin, Conor;
Nuka, Gift;
Pesseat, Sebastien;
Sangrador-Vegas, Amaia;
Scheremetjew, Maxim;
Rato, Claudia;
Yong, Siew-Yit;
Bateman, Alex;
Punta, Marco;
Attwood, Teresa K.;
Sigrist, Christian J.A.;
Redaschi, Nicole;
Rivoire, Catherine

Publication type:

Article

PredictProtein—an open resource for online prediction of protein structural and functional features.

Published in:

Nucleic Acids Research, 2014, v. 42, n. W1, p. W337, doi. 10.1093/nar/gku366

By:

Yachdav, Guy;
Kloppmann, Edda;
Kajan, Laszlo;
Hecht, Maximilian;
Goldberg, Tatyana;
Hamp, Tobias;
Hönigschmid, Peter;
Schafferhans, Andrea;
Roos, Manfred;
Bernhofer, Michael;
Richter, Lothar;
Ashkenazy, Haim;
Punta, Marco;
Schlessinger, Avner;
Bromberg, Yana;
Schneider, Reinhard;
Vriend, Gerrit;
Sander, Chris;
Ben-Tal, Nir;
Rost, Burkhard

Publication type:

Article

Pfam: the protein families database.

Published in:

Nucleic Acids Research, 2014, v. 42, n. D1, p. D222, doi. 10.1093/nar/gkt1223

By:

Finn, Robert D.;
Bateman, Alex;
Clements, Jody;
Coggill, Penelope;
Eberhardt, Ruth Y.;
Eddy, Sean R.;
Heger, Andreas;
Hetherington, Kirstie;
Holm, Liisa;
Mistry, Jaina;
Sonnhammer, Erik L. L.;
Tate, John;
Punta, Marco

Publication type:

Article

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions.

Published in:

Nucleic Acids Research, 2013, v. 41, n. 12, p. e121, doi. 10.1093/nar/gkt263

By:

Mistry, Jaina;
Finn, Robert D.;
Eddy, Sean R.;
Bateman, Alex;
Punta, Marco

Publication type:

Article

The Pfam protein families database.

Published in:

Nucleic Acids Research, 2012, p. D290, doi. 10.1093/nar/gkr1065

By:

Punta, Marco;
Coggill, Penny C.;
Eberhardt, Ruth Y.;
Mistry, Jaina;
Tate, John;
Boursnell, Chris;
Pang, Ningze;
Forslund, Kristoffer;
Ceric, Goran;
Clements, Jody;
Heger, Andreas;
Holm, Liisa;
Sonnhammer, Erik L. L.;
Eddy, Sean R.;
Bateman, Alex;
Finn, Robert D.

Publication type:

Article

The challenge of increasing Pfam coverage of the human proteome.

Published in:

2013

By:

Mistry, Jaina;
Coggill, Penny;
Eberhardt, Ruth Y.;
Deiana, Antonio;
Giansanti, Andrea;
Finn, Robert D.;
Bateman, Alex;
Punta, Marco

Publication type:

Correction Notice

The challenge of increasing Pfam coverage of the human proteome.

Published in:

Database: The Journal of Biological Databases & Curation, 2013, v. 2013, p. 1, doi. 10.1093/database/bat023

By:

Mistry, Jaina;
Coggill, Penny;
Eberhardt, Ruth Y.;
Deiana, Antonio;
Giansanti, Andrea;
Finn, Robert D.;
Bateman, Alex;
Punta, Marco

Publication type:

Article

AntiFam: a tool to help identify spurious ORFs in protein annotation.

Published in:

Database: The Journal of Biological Databases & Curation, 2012, v. 2012, p. 1, doi. 10.1093/database/bas003

By:

Eberhardt, Ruth Y.;
Haft, Daniel H.;
Punta, Marco;
Martin, Maria;
O'Donovan, Claire;
Bateman, Alex

Publication type:

Article

DPCfam: Unsupervised protein family classification by Density Peak Clustering of large sequence datasets.

Published in:

PLoS Computational Biology, 2022, v. 18, n. 10, p. 1, doi. 10.1371/journal.pcbi.1010610

By:

Russo, Elena Tea;
Barone, Federico;
Bateman, Alex;
Cozzini, Stefano;
Punta, Marco;
Laio, Alessandro

Publication type:

Article

Author Correction: Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer.

Published in:

2020

By:

von Loga, Katharina;
Woolston, Andrew;
Punta, Marco;
Barber, Louise J.;
Griffiths, Beatrice;
Semiannikova, Maria;
Spain, Georgia;
Challoner, Benjamin;
Fenwick, Kerry;
Simon, Ronald;
Marx, Andreas;
Sauter, Guido;
Lise, Stefano;
Matthews, Nik;
Gerlinger, Marco

Publication type:

Correction Notice

Extreme intratumour heterogeneity and driver evolution in mismatch repair deficient gastro-oesophageal cancer.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-019-13915-7

By:

von Loga, Katharina;
Woolston, Andrew;
Punta, Marco;
Barber, Louise J.;
Griffiths, Beatrice;
Semiannikova, Maria;
Spain, Georgia;
Challoner, Benjamin;
Fenwick, Kerry;
Simon, Ronald;
Marx, Andreas;
Sauter, Guido;
Lise, Stefano;
Matthews, Nik;
Gerlinger, Marco

Publication type:

Article

The SHOCT Domain: A Widespread Domain Under-Represented in Model Organisms.

Published in:

PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0057848

By:

Eberhardt, Ruth Y.;
Bartholdson, S. Josefin;
Punta, Marco;
Bateman, Alex

Publication type:

Article

NMR Structure of Lipoprotein YxeF from Bacillus subtilis Reveals a Calycin Fold and Distant Homology with the Lipocalin Blc from Escherichia coli.

Published in:

PLoS ONE, 2012, v. 7, n. 6, p. e37404, doi. 10.1371/journal.pone.0037404

By:

Yibing Wu;
Punta, Marco;
Rong Xiao;
Acton, Thomas B.;
Sathyamoorthy, Bharathwaj;
Dey, Fabian;
Fischer, Markus;
Skerra, Arne;
Rost, Burkhard;
Montelione, Gaetano T.;
Szyperski, Thomas

Publication type:

Article

Improved Disorder Prediction by Combination of Orthogonal Approaches.

Published in:

PLoS ONE, 2009, v. 4, n. 2, p. 1, doi. 10.1371/journal.pone.0004433

By:

Schlessinger, Avner;
Punta, Marco;
Yachdav, Guy;
Kajan, Laszlo;
Rost, Burkhard

Publication type:

Article

Identification of single nucleotide variants using position-specific error estimation in deep sequencing data.

Published in:

BMC Medical Genomics, 2019, v. 12, n. 1, p. N.PAG, doi. 10.1186/s12920-019-0557-9

By:

Kleftogiannis, Dimitrios;
Punta, Marco;
Jayaram, Anuradha;
Sandhu, Shahneen;
Wong, Stephen Q.;
Gasi Tandefelt, Delila;
Conteduca, Vincenza;
Wetterskog, Daniel;
Attard, Gerhardt;
Lise, Stefano

Publication type:

Article

Solution NMR structures of proteins VPA0419 from Vibrio parahaemolyticus and yiiS from Shigella flexneri provide structural coverage for protein domain family PFAM 04175.

Published in:

Proteins, 2010, v. 78, n. 3, p. 779, doi. 10.1002/prot.22630

By:

Singarapu, Kiran Kumar;
Mills, Jeffrey L.;
Xiao, Rong;
Acton, Thomas;
Punta, Marco;
Fischer, Markus;
Honig, Barry;
Rost, Burkhard;
Montelione, Gaetano T.;
Szyperski, Thomas

Publication type:

Article

Structural genomics reveals EVE as a new ASCH/PUA-related domain.

Published in:

Proteins, 2009, v. 75, n. 3, p. 760, doi. 10.1002/prot.22287

By:

Bertonati, Claudia;
Punta, Marco;
Fischer, Markus;
Yachdav, Guy;
Forouhar, Farhad;
Zhou, Weihong;
Kuzin, Alexander P.;
Seetharaman, Jayaraman;
Abashidze, Mariam;
Ramelot, Theresa A.;
Kennedy, Michael A.;
Cort, John R.;
Belachew, Adam;
Hunt, John F.;
Tong, Liang;
Montelione, Gaetano T.;
Rost, Burkhard

Publication type:

Article

Identifying cysteines and histidines in transition-metal-binding sites using support vector machines and neural networks.

Published in:

Proteins, 2006, v. 65, n. 2, p. 305, doi. 10.1002/prot.21135

By:

Passerini, Andrea;
Punta, Marco;
Ceroni, Alessio;
Rost, Burkhard;
Frasconi, Paolo

Publication type:

Article

CASP6 assessment of contact prediction.

Published in:

Proteins, 2005, v. 61, n. S7, p. 214, doi. 10.1002/prot.20739

By:

Graña, Osvaldo;
Baker, David;
MacCallum, Robert M.;
Meiler, Jens;
Punta, Marco;
Rost, Burkhard;
Tress, Michael L.;
Valencia, Alfonso

Publication type:

Article

Molecular modeling studies on CNG channel from bovine retinal rod: A structural model of the cyclic nucleotide-binding domain.

Published in:

Proteins, 2003, v. 52, n. 3, p. 332, doi. 10.1002/prot.10324

By:

Marco Punta;
Andrea Cavalli

Publication type:

Article

A knowledge-based scale for amino acid membrane propensity.

Published in:

Proteins, 2003, v. 50, n. 1, p. 114, doi. 10.1002/prot.10247

By:

Punta, Marco;
Maritan, Amos

Publication type:

Article

Crystal structures of three representatives of a new Pfam family PF14869 (DUF4488) suggest they function in sugar binding/uptake.

Published in:

Protein Science: A Publication of the Protein Society, 2014, v. 23, n. 10, p. 1380, doi. 10.1002/pro.2522

By:

Kumar, Abhinav;
Punta, Marco;
Axelrod, Herbert L.;
Das, Debanu;
Farr, Carol L.;
Grant, Joanna C.;
Chiu, Hsiu‐Ju;
Miller, Mitchell D.;
Coggill, Penelope C.;
Klock, Heath E.;
Elsliger, Marc‐André;
Deacon, Ashley M.;
Godzik, Adam;
Lesley, Scott A.;
Wilson, Ian A.

Publication type:

Article