Browse by UCL people
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Number of items: 27.
Article
Adeyelu, Tolulope;
Bordin, Nicola;
Waman, Vaishali P;
Sadlej, Marta;
Sillitoe, Ian;
Moya-Garcia, Aurelio A;
Orengo, Christine A;
(2023)
KinFams: De-Novo Classification of Protein Kinases Using CATH Functional Units.
Biomolecules
, 13
(2)
, Article 277. 10.3390/biom13020277.
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Bertoni, Damian;
Tsenkov, Maxim;
Magana, Paulyna;
Nair, Sreenath;
Pidruchna, Ivanna;
Querino Lima Afonso, Marcelo;
Midlik, Adam;
... Velankar, Sameer; + view all
(2025)
AlphaFold Protein Structure Database 2025: a redesigned interface and updated structural coverage.
Nucleic Acids Research
, Article gkaf1226. 10.1093/nar/gkaf1226.
(In press).
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Blum, Matthias;
Andreeva, Antonina;
Florentino, Laise Cavalcanti;
Chuguransky, Sara Rocio;
Grego, Tiago;
Hobbs, Emma;
Pinto, Beatriz Lazaro;
... Bateman, Alex; + view all
(2024)
InterPro: the protein sequence classification resource in 2025.
Nucleic Acids Research
, Article gkae1082. 10.1093/nar/gkae1082.
(In press).
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Bordin, Nicola;
Dallago, Christian;
Heinzinger, Michael;
Kim, Stephanie;
Littmann, Maria;
Rauer, Clemens;
Steinegger, Martin;
... Orengo, Christine; + view all
(2022)
Novel machine learning approaches revolutionize protein knowledge.
Trends in Biochemical Sciences
10.1016/j.tibs.2022.11.001.
(In press).
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Bordin, Nicola;
Lau, Andy M;
Orengo, Christine;
(2023)
Large-scale clustering of AlphaFold2 3D models shines light on the structure and function of proteins.
Molecular Cell
, 83
(22)
pp. 3950-3952.
10.1016/j.molcel.2023.10.039.
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Bordin, Nicola;
Sillitoe, Ian;
Nallapareddy, Vamsi;
Rauer, Clemens;
Lam, Su Datt;
Waman, Vaishali P;
Sen, Neeladri;
... Orengo, Christine; + view all
(2023)
AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms.
Communications Biology
, 6
(1)
, Article 160. 10.1038/s42003-023-04488-9.
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Bordin, N;
Carlos Gonzalez-Sanchez, J;
Devos, DP;
(2018)
PVCbase: an integrated web resource for the PVC bacterial proteomes.
Database
, 2018
, Article bay042. 10.1093/database/bay042.
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Bordin, N;
Sillitoe, I;
Lees, JG;
Orengo, C;
(2021)
Tracing Evolution Through Protein Structures: Nature Captured in a Few Thousand Folds.
Frontiers in Molecular Neuroscience
, 8
, Article 668184. 10.3389/fmolb.2021.668184.
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Crisci, MA;
Corsini, PM;
Bordin, N;
Chen, LX;
Banfield, JF;
Santini, JM;
(2022)
Detection and enumeration of Lak megaphages in microbiome samples by endpoint and quantitative PCR.
STAR Protocols
, 3
(1)
10.1016/j.xpro.2021.101029.
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Crisci, MA;
Chen, L-X;
Devoto, AE;
Borges, AL;
Bordin, N;
Sachdeva, R;
Tett, A;
... Santini, JM; + view all
(2021)
Closely related Lak megaphages replicate in the microbiomes of diverse animals.
iScience
, Article 102875. 10.1016/j.isci.2021.102875.
(In press).
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Heinzinger, Michael;
Littmann, Maria;
Sillitoe, Ian;
Bordin, Nicola;
Orengo, Christine;
Rost, Burkhard;
(2022)
Contrastive learning on protein embeddings enlightens midnight zone.
NAR Genomics and Bioinformatics
, 4
(2)
, Article lqac043. 10.1093/nargab/lqac043.
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Lam, SD;
Bordin, N;
Waman, VP;
Scholes, HM;
Ashford, P;
Sen, N;
van Dorp, L;
... Orengo, CA; + view all
(2020)
SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.
Scientific Reports
, 10
, Article 16471. 10.1038/s41598-020-71936-5.
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Littmann, M;
Bordin, N;
Heinzinger, M;
Schütze, K;
Dallago, C;
Orengo, C;
Rost, B;
(2021)
Clustering FunFams using sequence embeddings improves EC purity.
Bioinformatics
, 37
(20)
pp. 3449-3455.
10.1093/bioinformatics/btab371.
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Nallapareddy, Vamsi;
Bordin, Nicola;
Sillitoe, Ian;
Heinzinger, Michael;
Littmann, Maria;
Waman, Vaishali P;
Sen, Neeladri;
... Orengo, Christine; + view all
(2023)
CATHe: Detection of remote homologues for CATH superfamilies using embeddings from protein language models.
Bioinformatics
, 39
(1)
, Article btad029. 10.1093/bioinformatics/btad029.
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Nigris, S;
Baldan, E;
Tondello, A;
Zanella, F;
Vitulo, N;
Favaro, G;
Guidolin, V;
... Baldan, B; + view all
(2018)
Biocontrol traits of Bacillus licheniformis GL174, a culturable endophyte of Vitis vinifera cv. Glera.
BMC Microbiology
, 18
, Article 133. 10.1186/s12866-018-1306-5.
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O'Donoghue, SI;
Schafferhans, A;
Sikta, N;
Stolte, C;
Kaur, S;
Ho, BK;
Anderson, S;
... Rost, B; + view all
(2021)
SARS-CoV-2 structural coverage map reveals viral protein assembly, mimicry, and hijacking mechanisms.
Molecular Systems Biology
, 17
(9)
, Article e10079. 10.15252/msb.202010079.
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Øvreås, Lise;
Kallscheuer, Nicolai;
Calisto, Rita;
Bordin, Nicola;
Storesund, Julia E;
Jogler, Christian;
Devos, Damien;
(2024)
Comparative genomic analyses of aerobic planctomycetes isolated from the deep sea and the ocean surface.
Antonie Van Leeuwenhoek
, 118
, Article 33. 10.1007/s10482-024-02041-0.
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Rodríguez-López, María;
Bordin, Nicola;
Lees, Jon;
Scholes, Harry;
Hassan, Shaimaa;
Saintain, Quentin;
Kamrad, Stephan;
... Bähler, Jürg; + view all
(2023)
Broad functional profiling of fission yeast proteins using phenomics and machine learning.
eLife
, 12
10.7554/elife.88229.3.
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Sen, Neeladri;
Anishchenko, Ivan;
Bordin, Nicola;
Sillitoe, Ian;
Velankar, Sameer;
Baker, David;
Orengo, Christine;
(2022)
Characterizing and explaining the impact of disease-associated mutations in proteins without known structures or structural homologs.
Briefings in Bioinformatics
10.1093/bib/bbac187.
(In press).
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Sillitoe, I;
Bordin, N;
Dawson, N;
Waman, VP;
Ashford, P;
Scholes, HM;
Pang, CSM;
... Orengo, CA; + view all
(2020)
CATH: increased structural coverage of functional space.
Nucleic Acids Research
10.1093/nar/gkaa1079.
(In press).
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Singh, R;
Manivannan, S;
Krikken, AM;
de Boer, R;
Bordin, N;
Devos, DP;
van der Klei, IJ;
(2019)
Hansenula polymorpha Pex37 is a peroxisomal membrane protein required for organelle fission and segregation.
The FEBS Journal
10.1111/febs.15123.
(In press).
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Varadi, M;
Bordin, N;
Orengo, C;
Velankar, S;
(2023)
The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors.
Current Opinion in Structural Biology
, 79
, Article 102543. 10.1016/j.sbi.2023.102543.
(In press).
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Waman, Vaishali P;
Bordin, Nicola;
Alcraft, Rachel;
Vickerstaff, Robert;
Rauer, Clemens;
Chan, Qian;
Sillitoe, Ian;
... Orengo, Christine; + view all
(2024)
CATH 2024: CATH-AlphaFlow Doubles the Number of Structures in CATH and Reveals Nearly 200 New Folds.
Journal of Molecular Biology
, Article 168551. 10.1016/j.jmb.2024.168551.
(In press).
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Waman, Vaishali P;
Bordin, Nicola;
Lau, Andy;
Kandathil, Shaun;
Wells, Jude;
Miller, David;
Velankar, Sameer;
... Orengo, Christine; + view all
(2024)
CATH v4.4: major expansion of CATH by experimental and predicted structural data.
Nucleic Acids Research
, Article gkae1087. 10.1093/nar/gkae1087.
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Waman, VP;
Ashford, P;
Lam, SD;
Sen, N;
Abbasian, M;
Woodridge, L;
Goldtzvik, Y;
... Orengo, CA; + view all
(2024)
Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics.
Scientific Reports
, 14
, Article 14208. 10.1038/s41598-024-61541-1.
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Wu, F;
de Boer, R;
Krikken, AM;
Aksit, A;
Bordin, N;
Devos, DP;
van der Klei, IJ;
(2020)
Pex24 and Pex32 are required to tether peroxisomes to the ER for organelle biogenesis, positioning and segregation in yeast.
Journal of Cell Science
, 133
(16)
, Article jcs246983. 10.1242/jcs.246983.
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Working / discussion paper
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Lam, SD;
Bordin, N;
Waman, VP;
Scholes, HM;
Ashford, P;
Sen, N;
van Dorp, L;
... Orengo, CA; + view all
(2020)
SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals.
BioRxiv: Cold Spring Harbor, NY, USA.
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