BORDIN, NICOLA
BORDIN, NICOLA
Dipartimento di Scienze Biomediche - DSB
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage
2026 Bertoni, D.; Tsenkov, M.; Magana, P.; Nair, S.; Pidruchna, I.; Querino Lima Afonso, M.; Midlik, A.; Paramval, U.; Lawal, D.; Tanweer, A.; Last, M.; Patel, R.; Laydon, A.; Lasecki, D.; Dietrich, N.; Tomlinson, H.; Zidek, A.; Green, T.; Kovalevskiy, O.; Lau, A.; Kandathil, S.; Bordin, N.; Sillitoe, I.; Mirdita, M.; Jones, D.; Orengo, C.; Steinegger, M.; Fleming, J. R.; Velankar, S.
CATH v4.4: Major expansion of CATH by experimental and predicted structural data
2025 Waman, V. P.; Bordin, N.; Lau, A.; Kandathil, S.; Wells, J.; Miller, D.; Velankar, S.; Jones, D. T.; Sillitoe, I.; Orengo, C.
Comparative genomic analyses of aerobic planctomycetes isolated from the deep sea and the ocean surface
2025 Ovreas, L.; Kallscheuer, N.; Calisto, R.; Bordin, N.; Storesund, J. E.; Jogler, C.; Devos, D.; Lage, O.
CATH 2024: CATH-AlphaFlow Doubles the Number of Structures in CATH and Reveals Nearly 200 New Folds
2024 Waman, V. P.; Bordin, N.; Alcraft, R.; Vickerstaff, R.; Rauer, C.; Chan, Q.; Sillitoe, I.; Yamamori, H.; Orengo, C.
Chainsaw: protein domain segmentation with fully convolutional neural networks
2024 Wells, J.; Hawkins-Hooker, A.; Bordin, N.; Sillitoe, I.; Paige, B.; Orengo, C.
Clustering protein functional families at large scale with hierarchical approaches
2024 Bordin, N.; Scholes, H.; Rauer, C.; Roca-Martinez, J.; Sillitoe, I.; Orengo, C.
Exploring structural diversity across the protein universe with The Encyclopedia of Domains
2024 Lau, A. M.; Bordin, N.; Kandathil, S. M.; Sillitoe, I.; Waman, V. P.; Wells, J.; Orengo, C. A.; Jones, D. T.
Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics
2024 Waman, V. P.; Ashford, P.; Lam, S. D.; Sen, N.; Abbasian, M.; Woodridge, L.; Goldtzvik, Y.; Bordin, N.; Wu, J.; Sillitoe, I.; Orengo, C. A.
Quest for Orthologs in the Era of Biodiversity Genomics
2024 Langschied, F.; Bordin, N.; Cosentino, S.; Fuentes-Palacios, D.; Glover, N.; Hiller, M.; Hu, Y.; Huerta-Cepas, J.; Coelho, L. P.; Iwasaki, W.; Majidian, S.; Manzano-Morales, S.; Persson, E.; Richards, T. A.; Gabaldon, T.; Sonnhammer, E.; Thomas, P. D.; Dessimoz, C.; Ebersberger, I.
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms
2023 Bordin, N.; Sillitoe, I.; Nallapareddy, V.; Rauer, C.; Lam, S. D.; Waman, V. P.; Sen, N.; Heinzinger, M.; Littmann, M.; Kim, S.; Velankar, S.; Steinegger, M.; Rost, B.; Orengo, C.
Broad functional profiling of fission yeast proteins using phenomics and machine learning
2023 Rodriguez-Lopez, M.; Bordin, N.; Lees, J.; Scholes, H.; Hassan, S.; Saintain, Q.; Kamrad, S.; Orengo, C.; Bahler, J.
CATHe: detection of remote homologues for CATH superfamilies using embeddings from protein language models
2023 Nallapareddy, V.; Bordin, N.; Sillitoe, I.; Heinzinger, M.; Littmann, M.; Waman, V. P.; Sen, N.; Rost, B.; Orengo, C.
Decarboxylase Enzymes in the Polyamine Biosynthetic Pathway are Posttranslationally Modified by Lysine Acetyltransferase Proteins
2023 Glenn, Kp; Do, H; Bordin, N; Orengo, C; Kuhn, M
Insight Into the Structural Evolution of Polyamine Acetyltransferases Across Prokaryotes, Eukaryotes, and Archaea
2023 Do, H; Bordin, N; Rauer, C; Orengo, C; Kuhn, M
KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units
2023 Adeyelu, T.; Bordin, N.; Waman, V. P.; Sadlej, M.; Sillitoe, I.; Moya-Garcia, A. A.; Orengo, C. A.
Large-scale clustering of AlphaFold2 3D models shines light on the structure and function of proteins
2023 Bordin, N.; Lau, A. M.; Orengo, C.
Novel machine learning approaches revolutionize protein knowledge
2023 Bordin, N.; Dallago, C.; Heinzinger, M.; Kim, S.; Littmann, M.; Rauer, C.; Steinegger, M.; Rost, B.; Orengo, C.
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors
2023 Varadi, M.; Bordin, N.; Orengo, C.; Velankar, S.
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs
2022 Sen, N.; Anishchenko, I.; Bordin, N.; Sillitoe, I.; Velankar, S.; Baker, D.; Orengo, C.
Contrastive learning on protein embeddings enlightens midnight zone
2022 Heinzinger, M.; Littmann, M.; Sillitoe, I.; Bordin, N.; Orengo, C.; Rost, B.