Works by Marcatili, Paolo

Results: 48

Variability analysis of LC-MS experimental factors and their impact on machine learning.

Published in:

GigaScience, 2023, v. 12, n. 1, p. 1, doi. 10.1093/gigascience/giad096

By:

Rehfeldt, Tobias Greisager;
Krawczyk, Konrad;
Echers, Simon Gregersen;
Marcatili, Paolo;
Palczynski, Pawel;
Röttger, Richard;
Schwämmle, Veit

Publication type:

Article

DiscoTope-3.0: improved B-cell epitope prediction using inverse folding latent representations.

Published in:

Frontiers in Immunology, 2024, p. 1, doi. 10.3389/fimmu.2024.1322712

By:

Høie, Magnus Haraldson;
Gade, Frederik Steensgaard;
Johansen, Julie Maria;
Würtzen, Charlotte;
Winther, Ole;
Nielsen, Morten;
Marcatili, Paolo

Publication type:

Article

The Protein‐Templated Synthesis of Enzyme‐Generated Aptamers.

Published in:

Angewandte Chemie, 2022, v. 134, n. 17, p. 1, doi. 10.1002/ange.202201061

By:

Vacacela, Julio;
Schaap‐Johansen, Anna‐Lisa;
Manikova, Patricia;
Marcatili, Paolo;
Prado, Marta;
Sun, Yi;
Ashley, Jon

Publication type:

Article

A database of immunoglobulins with integrated tools: DIGIT.

Published in:

Nucleic Acids Research, 2012, p. D1230, doi. 10.1093/nar/gkr806

By:

Chailyan, Anna;
Tramontano, Anna;
Marcatili, Paolo

Publication type:

Article

The association of heavy and light chain variable domains in antibodies: implications for antigen specificity.

Published in:

FEBS Journal, 2011, v. 278, n. 16, p. 2858, doi. 10.1111/j.1742-4658.2011.08207.x

By:

Chailyan, Anna;
Marcatili, Paolo;
Tramontano, Anna

Publication type:

Article

Antibody Specific B-Cell Epitope Predictions: Leveraging Information From Antibody-Antigen Protein Complexes.

Published in:

Frontiers in Immunology, 2019, p. N.PAG, doi. 10.3389/fimmu.2019.00298

By:

Jespersen, Martin Closter;
Mahajan, Swapnil;
Peters, Bjoern;
Nielsen, Morten;
Marcatili, Paolo

Publication type:

Article

Epitope Specific Antibodies and T Cell Receptors in the Immune Epitope Database.

Published in:

Frontiers in Immunology, 2018, p. N.PAG, doi. 10.3389/fimmu.2018.02688

By:

Mahajan, Swapnil;
Vita, Randi;
Shackelford, Deborah;
Lane, Jerome;
Schulten, Veronique;
Zarebski, Laura;
Jespersen, Martin Closter;
Marcatili, Paolo;
Nielsen, Morten;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

ArrayPitope: Automated Analysis of Amino Acid Substitutions for Peptide Microarray-Based Antibody Epitope Mapping.

Published in:

PLoS ONE, 2017, v. 12, n. 1, p. 1, doi. 10.1371/journal.pone.0168453

By:

Hansen, Christian Skjødt;
Østerbye, Thomas;
Marcatili, Paolo;
Lund, Ole;
Buus, Søren;
Nielsen, Morten

Publication type:

Article

Human MHC-II with Shared Epitope Motifs Are Optimal Epstein-Barr Virus Glycoprotein 42 Ligands--Relation to Rheumatoid Arthritis.

Published in:

International Journal of Molecular Sciences, 2018, v. 19, n. 1, p. 317, doi. 10.3390/ijms19010317

By:

Trier, Nicole;
Izarzugaza, Jose;
Chailyan, Anna;
Marcatili, Paolo;
Houen, Gunnar

Publication type:

Article

Benchmark datasets of immune receptor-epitope structural complexes.

Published in:

BMC Bioinformatics, 2019, v. 20, n. 1, p. N.PAG, doi. 10.1186/s12859-019-3109-6

By:

Mahajan, Swapnil;
Yan, Zhen;
Jespersen, Martin Closter;
Jensen, Kamilla Kjærgaard;
Marcatili, Paolo;
Nielsen, Morten;
Sette, Alessandro;
Peters, Bjoern

Publication type:

Article

Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia.

Published in:

BMC Bioinformatics, 2018, v. 19, n. 14, p. 67, doi. 10.1186/s12859-018-2381-1

By:

Polychronidou, Eleftheria;
Kalamaras, Ilias;
Agathangelidis, Andreas;
Sutton, Lesley-Ann;
Yan, Xiao-Jie;
Bikos, Vasilis;
Vardi, Anna;
Mochament, Konstantinos;
Chiorazzi, Nicholas;
Belessi, Chrysoula;
Rosenquist, Richard;
Ghia, Paolo;
Stamatopoulos, Kostas;
Vlamos, Panayiotis;
Chailyan, Anna;
Overby, Nanna;
Marcatili, Paolo;
Hatzidimitriou, Anastasia;
Tzovaras, Dimitrios

Publication type:

Article

The Protein‐Templated Synthesis of Enzyme‐Generated Aptamers.

Published in:

Angewandte Chemie International Edition, 2022, v. 61, n. 17, p. 1, doi. 10.1002/anie.202201061

By:

Vacacela, Julio;
Schaap‐Johansen, Anna‐Lisa;
Manikova, Patricia;
Marcatili, Paolo;
Prado, Marta;
Sun, Yi;
Ashley, Jon

Publication type:

Article

BepiPred‐3.0: Improved B‐cell epitope prediction using protein language models.

Published in:

Protein Science: A Publication of the Protein Society, 2022, v. 31, n. 12, p. 1, doi. 10.1002/pro.4497

By:

Clifford, Joakim Nøddeskov;
Høie, Magnus Haraldson;
Deleuran, Sebastian;
Peters, Bjoern;
Nielsen, Morten;
Marcatili, Paolo

Publication type:

Article

Widespread amyloidogenicity potential of multiple myeloma patient-derived immunoglobulin light chains.

Published in:

BMC Biology, 2023, p. 1, doi. 10.1186/s12915-022-01506-w

By:

Sternke-Hoffmann, Rebecca;
Pauly, Thomas;
Norrild, Rasmus K.;
Hansen, Jan;
Tucholski, Florian;
Høie, Magnus Haraldson;
Marcatili, Paolo;
Dupré, Mathieu;
Duchateau, Magalie;
Rey, Martial;
Malosse, Christian;
Metzger, Sabine;
Boquoi, Amelie;
Platten, Florian;
Egelhaaf, Stefan U.;
Chamot-Rooke, Julia;
Fenk, Roland;
Nagel-Steger, Luitgard;
Haas, Rainer;
Buell, Alexander K.

Publication type:

Article

Tabhu: tools for antibody humanization.

Published in:

Bioinformatics, 2015, v. 31, n. 3, p. 434, doi. 10.1093/bioinformatics/btu667

By:

Olimpieri, Pier Paolo;
Marcatili, Paolo;
Tramontano, Anna

Publication type:

Article

Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies.

Published in:

Bioinformatics, 2014, v. 30, n. 19, p. 2733, doi. 10.1093/bioinformatics/btu194

By:

Messih, Mario Abdel;
Lepore, Rosalba;
Marcatili, Paolo;
Tramontano, Anna

Publication type:

Article

Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server.

Published in:

Bioinformatics, 2013, v. 29, n. 18, p. 2285, doi. 10.1093/bioinformatics/btt369

By:

Olimpieri, Pier Paolo;
Chailyan, Anna;
Tramontano, Anna;
Marcatili, Paolo

Publication type:

Article

MAISTAS: a tool for automatic structural evaluation of alternative splicing products.

Published in:

Bioinformatics, 2011, v. 27, n. 12, p. 1625, doi. 10.1093/bioinformatics/btr198

By:

Floris, Matteo;
Raimondo, Domenico;
Leoni, Guido;
Orsini, Massimiliano;
Marcatili, Paolo;
Tramontano, Anna

Publication type:

Article

PICMI: mapping point mutations on genomes.

Published in:

Bioinformatics, 2010, v. 26, n. 22, p. 2904, doi. 10.1093/bioinformatics/btq547

By:

Pera, Loredana Le;
Marcatili, Paolo;
Tramontano, Anna

Publication type:

Article

PIGS: automatic prediction of antibody structures.

Published in:

Bioinformatics, 2008, v. 24, n. 17, p. 1953, doi. 10.1093/bioinformatics/btn341

By:

Marcatili, Paolo;
Rosi, Alessandra;
Tramontano, Anna

Publication type:

Article

Identification of emulsifier potato peptides by bioinformatics: application to omega-3 delivery emulsions and release from potato industry side streams.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-019-57229-6

By:

García-Moreno, Pedro J.;
Gregersen, Simon;
Nedamani, Elham R.;
Olsen, Tobias H.;
Marcatili, Paolo;
Overgaard, Michael T.;
Andersen, Mogens L.;
Hansen, Egon B.;
Jacobsen, Charlotte

Publication type:

Article

TCRpMHCmodels: Structural modelling of TCR-pMHC class I complexes.

Published in:

Scientific Reports, 2019, v. 9, n. 1, p. N.PAG, doi. 10.1038/s41598-019-50932-4

By:

Jensen, Kamilla Kjærgaard;
Rantos, Vasileios;
Jappe, Emma Christine;
Olsen, Tobias Hegelund;
Jespersen, Martin Closter;
Jurtz, Vanessa;
Jessen, Leon Eyrich;
Lanzarotti, Esteban;
Mahajan, Swapnil;
Peters, Bjoern;
Nielsen, Morten;
Marcatili, Paolo

Publication type:

Article

NetSurfP‐2.0: Improved prediction of protein structural features by integrated deep learning.

Published in:

Proteins, 2019, v. 87, n. 6, p. 520, doi. 10.1002/prot.25674

By:

Klausen, Michael Schantz;
Jespersen, Martin Closter;
Nielsen, Henrik;
Jensen, Kamilla Kjærgaard;
Jurtz, Vanessa Isabell;
Sønderby, Casper Kaae;
Sommer, Morten Otto Alexander;
Winther, Ole;
Nielsen, Morten;
Petersen, Bent;
Marcatili, Paolo

Publication type:

Article

Structural repertoire of immunoglobulin λ light chains.

Published in:

Proteins, 2011, v. 79, n. 5, p. 1513, doi. 10.1002/prot.22979

By:

Chailyan, Anna;
Marcatili, Paolo;
Cirillo, Davide;
Tramontano, Anna

Publication type:

Article

Immunoglobulin G structure and rheumatoid factor epitopes.

Published in:

PLoS ONE, 2019, v. 14, n. 6, p. 1, doi. 10.1371/journal.pone.0217624

By:

Maibom-Thomsen, Sheila Lefoli;
Trier, Nicole Hartwig;
Holm, Bettina Eide;
Hansen, Kirsten Beth;
Rasmussen, Morten Ib;
Chailyan, Anna;
Marcatili, Paolo;
Højrup, Peter;
Houen, Gunnar

Publication type:

Article

Improved methods for predicting peptide binding affinity to MHC class II molecules.

Published in:

Immunology, 2018, v. 154, n. 3, p. 394, doi. 10.1111/imm.12889

By:

Jensen, Kamilla Kjærgaard;
Andreatta, Massimo;
Marcatili, Paolo;
Buus, Søren;
Greenbaum, Jason A.;
Yan, Zhen;
Sette, Alessandro;
Peters, Bjoern;
Nielsen, Morten

Publication type:

Article

FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S2-S2

By:

Ausiello, Gabriele;
Gherardini, Pier Federico;
Marcatili, Paolo;
Tramontano, Anna;
Via, Allegra;
Helmer-Citterich, Manuela

Publication type:

Article

The MoVIN server for the analysis of protein interaction networks.

Published in:

BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-S2-S11

By:

Marcatili, Paolo;
Bussotti, Giovanni;
Tramontano, Anna

Publication type:

Article

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

Published in:

PLoS Computational Biology, 2016, v. 12, n. 4, p. 1, doi. 10.1371/journal.pcbi.1004870

By:

Asti, Lorenzo;
Uguzzoni, Guido;
Marcatili, Paolo;
Pagnani, Andrea

Publication type:

Article

T Cell Epitope Prediction and Its Application to Immunotherapy.

Published in:

Frontiers in Immunology, 2021, v. 12, p. 1, doi. 10.3389/fimmu.2021.712488

By:

Schaap-Johansen, Anna-Lisa;
Vujović, Milena;
Borch, Annie;
Hadrup, Sine Reker;
Marcatili, Paolo

Publication type:

Article

NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning.

Published in:

Nucleic Acids Research, 2022, v. 50, n. W1, p. W510, doi. 10.1093/nar/gkac439

By:

Høie, Magnus Haraldson;
Kiehl, Erik Nicolas;
Petersen, Bent;
Nielsen, Morten;
Winther, Ole;
Nielsen, Henrik;
Hallgren, Jeppe;
Marcatili, Paolo

Publication type:

Article

Terminal deoxynucleotidyl transferase-mediated formation of protein binding polynucleotides.

Published in:

Nucleic Acids Research, 2021, v. 49, n. 2, p. 1065, doi. 10.1093/nar/gkaa1263

By:

Ashley, Jon;
Schaap-Johansen, Anna-Lisa;
Mohammadniaei, Mohsen;
Naseri, Maryam;
Marcatili, Paolo;
Prado, Marta;
Yi Sun

Publication type:

Article

The ABCD database: a repository for chemically defined antibodies.

Published in:

Nucleic Acids Research, 2020, v. 48, n. D1, p. D261, doi. 10.1093/nar/gkz714

By:

Lima, Wanessa C;
Gasteiger, Elisabeth;
Marcatili, Paolo;
Duek, Paula;
Bairoch, Amos;
Cosson, Pierre

Publication type:

Article

IEDB-AR: immune epitope database—analysis resource in 2019.

Published in:

Nucleic Acids Research, 2019, v. 47, n. W1, p. W502, doi. 10.1093/nar/gkz452

By:

Dhanda, Sandeep Kumar;
Mahajan, Swapnil;
Paul, Sinu;
Yan, Zhen;
Kim, Haeuk;
Jespersen, Martin Closter;
Jurtz, Vanessa;
Andreatta, Massimo;
Greenbaum, Jason A;
Marcatili, Paolo;
Sette, Alessandro;
Nielsen, Morten;
Peters, Bjoern

Publication type:

Article

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes.

Published in:

Nucleic Acids Research, 2017, v. 45, n. W1, p. W24, doi. 10.1093/nar/gkx346

By:

Jespersen, Martin Closter;
Peters, Bjoern;
Nielsen, Morten;
Marcatili, Paolo

Publication type:

Article

LYRA, a webserver for lymphocyte receptor structural modeling.

Published in:

Nucleic Acids Research, 2015, v. 43, n. W1, p. W349, doi. 10.1093/nar/gkv535

By:

Schantz Klausen, Michael;
Anderson, Mads Valdemar;
Closter Jespersen, Martin;
Nielsen, Morten;
Marcatili, Paolo

Publication type:

Article

AnOxPePred: using deep learning for the prediction of antioxidative properties of peptides.

Published in:

Scientific Reports, 2020, v. 10, n. 1, p. 1, doi. 10.1038/s41598-020-78319-w

By:

Olsen, Tobias Hegelund;
Yesiltas, Betül;
Marin, Frederikke Isa;
Pertseva, Margarita;
García-Moreno, Pedro J.;
Gregersen, Simon;
Overgaard, Michael Toft;
Jacobsen, Charlotte;
Lund, Ole;
Hansen, Egon Bech;
Marcatili, Paolo

Publication type:

Article

Erratum: Antibody structural modeling with prediction of immunoglobulin structure (PIGS).

Published in:

Nature Protocols, 2015, v. 10, n. 4, p. 644, doi. 10.1038/nprot0415-644e

By:

Marcatili, Paolo;
Olimpieri, Pier Paolo;
Chailyan, Anna;
Tramontano, Anna

Publication type:

Article

Antibody modeling using the Prediction of ImmunoGlobulin Structure (PIGS) web server.

Published in:

Nature Protocols, 2014, v. 9, n. 12, p. 2771, doi. 10.1038/nprot.2014.189

By:

Marcatili, Paolo;
Olimpieri, Pier Paolo;
Chailyan, Anna;
Tramontano, Anna

Publication type:

Article

On the Mechanism of Chloroquine Resistance in Plasmodium falciparum.

Published in:

PLoS ONE, 2010, v. 5, n. 11, p. 1, doi. 10.1371/journal.pone.0014064

By:

Chinappi, Mauro;
Via, Allegra;
Marcatili, Paolo;
Tramontano, Anna

Publication type:

Article

Mutation Pattern of Paired Immunoglobulin Heavy and Light Variable Domains in Chronic Lymphocytic Leukemia B Cells.

Published in:

Molecular Medicine, 2011, v. 17, n. 11/12, p. 1188, doi. 10.2119/molmed.2011.00104

By:

Ghiotto, Fabio;
Marcatili, Paolo;
Tenca, Claudya;
Calevo, Maria Grazia;
Xiao-Jie Yan;
Albesiano, Emilia;
Bagnara, Davide;
Colombo, Monica;
Cutrona, Giovanna;
Chu, Charles C.;
Morabito, Fortunato;
Bruno, Silvia;
Ferrarini, Manlio;
Tramontano, Anna;
Fais, Franco;
Chiorazzi, Nicholas

Publication type:

Article

Signatures of T cell immunity revealed using sequence similarity with TCRDivER algorithm.

Published in:

Communications Biology, 2023, v. 6, n. 1, p. 1, doi. 10.1038/s42003-023-04702-8

By:

Vujović, Milena;
Marcatili, Paolo;
Chain, Benny;
Kaplinsky, Joseph;
Andresen, Thomas Lars

Publication type:

Article

T-Cell Receptor Cognate Target Prediction Based on Paired α and β Chain Sequence and Structural CDR Loop Similarities.

Published in:

Frontiers in Immunology, 2019, p. 1, doi. 10.3389/fimmu.2019.02080

By:

Lanzarotti, Esteban;
Marcatili, Paolo;
Nielsen, Morten

Publication type:

Article

Biofunctionality of Enzymatically Derived Peptides from Codfish (Gadus morhua) Frame: Bulk In Vitro Properties, Quantitative Proteomics, and Bioinformatic Prediction.

Published in:

Marine Drugs, 2020, v. 18, n. 12, p. 599, doi. 10.3390/md18120599

By:

Jafarpour, Ali;
Gregersen, Simon;
Marciel Gomes, Rocio;
Marcatili, Paolo;
Hegelund Olsen, Tobias;
Jacobsen, Charlotte;
Overgaard, Michael Toft;
Sørensen, Ann-Dorit Moltke

Publication type:

Article

A novel approach to probe host-pathogen interactions of bovine digital dermatitis, a model of a complex polymicrobial infection.

Published in:

BMC Genomics, 2016, v. 17, p. 1, doi. 10.1186/s12864-016-3341-7

By:

Marcatili, Paolo;
Nielsen, Martin W.;
Sicheritz-Pontén, Thomas;
Jensen, Tim K.;
Schafer-Nielsen, Claus;
Boye, Mette;
Nielsen, Morten;
Klitgaard, Kirstine

Publication type:

Article

Comparative Structure Analysis of the Multi-Domain, Cell Envelope Proteases of Lactic Acid Bacteria.

Published in:

Microorganisms, 2023, v. 11, n. 9, p. 2256, doi. 10.3390/microorganisms11092256

By:

Christensen, Lise Friis;
Høie, Magnus Haraldson;
Bang-Berthelsen, Claus Heiner;
Marcatili, Paolo;
Hansen, Egon Bech

Publication type:

Article

Data mining patented antibody sequences.

Published in:

2021

By:

Krawczyk, Konrad;
Buchanan, Andrew;
Marcatili, Paolo

Publication type:

Report

T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes.

Published in:

Nature Biotechnology, 2018, v. 36, n. 12, p. 1191, doi. 10.1038/nbt.4303

By:

Bentzen, Amalie K;
Such, Lina;
Jensen, Kamilla K;
Marquard, Andrea M;
Jessen, Leon E;
Miller, Natalie J;
Church, Candice D;
Lyngaa, Rikke;
Koelle, David M;
Becker, Jürgen C;
Linnemann, Carsten;
Schumacher, Ton N M;
Marcatili, Paolo;
Nghiem, Paul;
Nielsen, Morten;
Hadrup, Sine R

Publication type:

Article