| BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes MC Jespersen, B Peters, M Nielsen, P Marcatili Nucleic acids research 45 (W1), W24-W29, 2017 | 1520 | 2017 |
| NetMHCpan-4.0: improved peptide–MHC class I interaction predictions integrating eluted ligand and peptide binding affinity data V Jurtz, S Paul, M Andreatta, P Marcatili, B Peters, M Nielsen The Journal of Immunology 199 (9), 3360-3368, 2017 | 1403 | 2017 |
| Improved methods for predicting peptide binding affinity to MHC class II molecules KK Jensen, M Andreatta, P Marcatili, S Buus, JA Greenbaum, Z Yan, ... Immunology 154 (3), 394-406, 2018 | 812 | 2018 |
| DeepTMHMM predicts alpha and beta transmembrane proteins using deep neural networks J Hallgren, KD Tsirigos, MD Pedersen, JJ Almagro Armenteros, ... BioRxiv, 2022.04. 08.487609, 2022 | 770 | 2022 |
| NetSurfP‐2.0: Improved prediction of protein structural features by integrated deep learning MS Klausen, MC Jespersen, H Nielsen, KK Jensen, VI Jurtz, ... Proteins: Structure, Function, and Bioinformatics 87 (6), 520-527, 2019 | 594 | 2019 |
| IEDB-AR: immune epitope database—analysis resource in 2019 SK Dhanda, S Mahajan, S Paul, Z Yan, H Kim, MC Jespersen, V Jurtz, ... Nucleic acids research 47 (W1), W502-W506, 2019 | 349 | 2019 |
| PIGS: automatic prediction of antibody structures P Marcatili, A Rosi, A Tramontano Bioinformatics 24 (17), 1953-1954, 2008 | 201 | 2008 |
| NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning MH Høie, EN Kiehl, B Petersen, M Nielsen, O Winther, H Nielsen, ... Nucleic acids research 50 (W1), W510-W515, 2022 | 175 | 2022 |
| Antibody specific B-cell epitope predictions: leveraging information from antibody-antigen protein complexes MC Jespersen, S Mahajan, B Peters, M Nielsen, P Marcatili Frontiers in immunology 10, 298, 2019 | 140 | 2019 |
| On the mechanism of chloroquine resistance in Plasmodium falciparum M Chinappi, A Via, P Marcatili, A Tramontano PloS one 5 (11), e14064, 2010 | 130 | 2010 |
| The association of heavy and light chain variable domains in antibodies: implications for antigen specificity A Chailyan, P Marcatili, A Tramontano FEBS Journal, 2011 | 129 | 2011 |
| AnOxPePred: using deep learning for the prediction of antioxidative properties of peptides TH Olsen, B Yesiltas, FI Marin, M Pertseva, PJ García-Moreno, ... Scientific reports 10 (1), 21471, 2020 | 125 | 2020 |
| BepiPred‐3.0: Improved B‐cell epitope prediction using protein language models JN Clifford, MH Høie, S Deleuran, B Peters, M Nielsen, P Marcatili Protein Science 31 (12), e4497, 2022 | 120 | 2022 |
| Stereotyped patterns of B-cell receptor in splenic marginal zone lymphoma S Zibellini, D Capello, F Forconi, P Marcatili, D Rossi, S Rattotti, ... haematologica, haematol. 2010.025437 v1, 2010 | 113 | 2010 |
| Prediction of site-specific interactions in antibody-antigen complexes: the proABC method and server PP Olimpieri, A Chailyan, A Tramontano, P Marcatili Bioinformatics 29 (18), 2285-2291, 2013 | 112 | 2013 |
| NetTCR: sequence-based prediction of TCR binding to peptide-MHC complexes using convolutional neural networks VI Jurtz, LE Jessen, AK Bentzen, MC Jespersen, S Mahajan, R Vita, ... BioRxiv, 433706, 2018 | 106 | 2018 |
| T cell receptor fingerprinting enables in-depth characterization of the interactions governing recognition of peptide–MHC complexes AK Bentzen, L Such, KK Jensen, AM Marquard, LE Jessen, NJ Miller, ... Nature biotechnology 36 (12), 1191-1196, 2018 | 101 | 2018 |
| Immunoglobulin G structure and rheumatoid factor epitopes SL Maibom-Thomsen, NH Trier, BE Holm, KB Hansen, MI Rasmussen, ... PLoS One 14 (6), e0217624, 2019 | 97 | 2019 |
| The ABCD database: a repository for chemically defined antibodies WC Lima, E Gasteiger, P Marcatili, P Duek, A Bairoch, P Cosson Nucleic acids research 48 (D1), D261-D264, 2020 | 88 | 2020 |
| Antibody informatics for drug discovery H Shirai, C Prades, R Vita, P Marcatili, B Popovic, J Xu, JP Overington, ... Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1844 (11), 2002-2015, 2014 | 86 | 2014 |
Morten NielsenDepartment of Health Technology, The Technical University ofVerified email at cbs.dtu.dk
