Browse by UCL people
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Number of items: 39.
Article
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, M;
Chang, H-Y;
Chuguransky, S;
Grego, T;
Kandasaamy, S;
Mitchell, A;
Nuka, G;
... Finn, RD; + view all
(2020)
The InterPro protein families and domains database: 20 years on.
Nucleic Acids Research
10.1093/nar/gkaa977.
(In press).
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Das, S;
Lee, D;
Sillitoe, I;
Dawson, NL;
Lees, JG;
Orengo, CA;
(2015)
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.
Bioinformatics
, 31
(21)
pp. 3460-3467.
10.1093/bioinformatics/btv398.
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Das, S;
Sillitoe, I;
Lee, D;
Lees, JG;
Dawson, NL;
Ward, J;
Orengo, CA;
(2015)
CATH FunFHMMer web server: protein functional annotations using functional family assignments.
Nucleic Acids Res
, 43
(W1)
W148-W153.
10.1093/nar/gkv488.
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Dawson, NL;
Lewis, TE;
Das, S;
Lees, JG;
Lee, D;
Ashford, P;
Orengo, CA;
(2017)
CATH: an expanded resource to predict protein function through structure and sequence.
Nucleic Acids Research
, 45
(D1)
D289-D295.
10.1093/nar/gkw1098.
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Finn, RD;
Attwood, TK;
Babbitt, PC;
Bateman, A;
Bork, P;
Bridge, AJ;
Chang, HY;
... Mitchell, AL; + view all
(2016)
InterPro in 2017-beyond protein family and domain annotations.
Nucleic Acids Research
10.1093/nar/gkw1107.
(In press).
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Furnham, N;
Sillitoe, I;
Holliday, GL;
Cuff, AL;
Laskowski, RA;
Orengo, CA;
Thornton, JM;
(2012)
Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies.
PLoS Comput Biol
, 8
(3)
, Article e1002403. 10.1371/journal.pcbi.1002403.
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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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Jiang, Y;
Oron, TR;
Clark, WT;
Bankapur, AR;
D'Andrea, D;
Lepore, R;
Funk, CS;
... Radivojac, P; + view all
(2016)
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Genome Biology
, 17
, Article 184. 10.1186/s13059-016-1037-6.
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Lam, SD;
Das, S;
Sillitoe, I;
Orengo, C;
(2017)
An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences.
Acta Crystallographica Section D
, 73
pp. 628-640.
10.1107/S2059798317008920.
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Lam, SD;
Dawson, NL;
Das, S;
Sillitoe, I;
Ashford, P;
Lee, D;
Lehtinen, S;
... Lees, JG; + view all
(2016)
Gene3D: expanding the utility of domain assignments.
Nucleic Acids Res
, 44
(D1)
D404-D409.
10.1093/nar/gkv1231.
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Laskowski, RA;
Stephenson, JD;
Sillitoe, I;
Orengo, CA;
Thornton, JM;
(2020)
VarSite: disease variants and protein structure.
Protein Science
, 29
(1)
pp. 111-119.
10.1002/pro.3746.
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Lees, JG;
Dawson, NL;
Sillitoe, I;
Orengo, CA;
(2016)
Functional innovation from changes in protein domains and their combinations.
Current Opinion in Structural Biology
, 38
pp. 44-52.
10.1016/j.sbi.2016.05.016.
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Lees, JG;
Lee, D;
Studer, RA;
Dawson, NL;
Sillitoe, I;
Das, S;
Yeats, C;
... Orengo, CA; + view all
(2013)
Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.
Nucleic Acids Research
, 42
(D1)
D240-D245.
10.1093/nar/gkt1205.
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Lewis, T;
Sillitoe, I;
Dawson, N;
Lam, SD;
Clarke, T;
Lee, D;
Orengo, C;
(2017)
Gene3D: Extensive prediction of globular domains in proteins.
Nucleic Acids Research
, Article gkx1069. 10.1093/nar/gkx1069/4588111.
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Lewis, TE;
Sillitoe, I;
Andreeva, A;
Blundell, TL;
Buchan, DW;
Chothia, C;
Cozzetto, D;
... Orengo, C; + view all
(2014)
Genome3D: exploiting structure to help users understand their sequences.
Nucleic Acids Research
, 43
(D1)
D382-D386.
10.1093/nar/gku973.
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Lewis, TE;
Sillitoe, I;
Andreeva, A;
Blundell, TL;
Buchan, DW;
Chothia, C;
Cuff, A;
... Orengo, C; + view all
(2013)
Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.
Nucleic Acids Research
, 41
(Databa)
D499 - D507.
10.1093/nar/gks1266.
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Lewis, TE;
Sillitoe, I;
Dawson, N;
Lam, SD;
Clarke, T;
Lee, D;
Orengo, C;
(2017)
Gene3D: Extensive prediction of globular domains in proteins.
[Corrigendum].
Nucleic Acids Research
10.1093/nar/gkx1187.
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Lewis, TE;
Sillitoe, I;
Lees, JG;
(2018)
cath-resolve-hits: a new tool that resolves domain matches suspiciously quickly.
Bioinformatics
, 35
(10)
pp. 1766-1767.
10.1093/bioinformatics/bty863.
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Mitchell, AL;
Attwood, TK;
Babbitt, PC;
Blum, M;
Bork, P;
Bridge, A;
Brown, SD;
... Finn, RD; + view all
(2018)
InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
Nucleic Acids Research
10.1093/nar/gky1100.
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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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Paysan-Lafosse, Typhaine;
Blum, Matthias;
Chuguransky, Sara;
Grego, Tiago;
Pinto, Beatriz Lázaro;
Salazar, Gustavo A;
Bileschi, Maxwell L;
... Bateman, Alex; + view all
(2023)
InterPro in 2022.
Nucleic Acids Research
, 51
(D1)
D418-D427.
10.1093/nar/gkac993.
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Redfern, OC;
Dessailly, BH;
Dallman, TJ;
Sillitoe, I;
Orengo, CA;
(2009)
FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies.
PLOS COMPUT BIOL
, 5
(8)
, Article e1000485. 10.1371/journal.pcbi.1000485.
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Sillitoe, I;
Andreeva, A;
Blundell, TL;
Buchan, DWA;
Finn, RD;
Gough, J;
Jones, D;
... Orengo, C; + view all
(2019)
Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation.
Nucleic Acids Research
10.1093/nar/gkz967.
(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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Sillitoe, I;
Dawson, N;
Lewis, TE;
Das, S;
Lees, JG;
Ashford, P;
Tolulope, A;
... Orengo, CA; + view all
(2019)
CATH: expanding the horizons of structure-based functional annotations for genome sequences.
Nucleic Acids Research
, 47
(D1)
D280-D284.
10.1093/nar/gky1097.
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Sillitoe, I;
Dawson, N;
Thornton, J;
Orengo, C;
(2015)
The history of the CATH structural classification of protein domains.
Biochimie
, 119
pp. 209-217.
10.1016/j.biochi.2015.08.004.
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Sillitoe, I;
Furnham, N;
(2016)
FunTree: advances in a resource for exploring and contextualising protein function evolution.
Nucleic Acids Research
, 44
(D1)
D317-D323.
10.1093/nar/gkv1274.
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Sillitoe, I;
Lewis, TE;
Cuff, A;
Das, S;
Ashford, P;
Dawson, NL;
Furnham, N;
... Orengo, CA; + view all
(2014)
CATH: comprehensive structural and functional annotations for genome sequences.
Nucleic Acids Research
, 43
(D1)
D376-D381.
10.1093/nar/gku947.
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Tordai, Hedvig;
Suhajda, Erzsebet;
Sillitoe, Ian;
Nair, Sreenath;
Varadi, Mihaly;
Hegedus, Tamas;
(2022)
Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology.
International Journal of Molecular Sciences
, 23
(16)
, Article 8877. 10.3390/ijms23168877.
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Tyzack, JD;
Furnham, N;
Sillitoe, I;
Orengo, CM;
Thornton, JM;
(2019)
Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.
Methods in Molecular Biology
, 1851
pp. 263-275.
10.1007/978-1-4939-8736-8_14.
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Tyzack, JD;
Furnham, N;
Sillitoe, I;
Orengo, CM;
Thornton, JM;
(2017)
Understanding enzyme function evolution from a computational perspective.
Curr Opin Struct Biol
, 47
pp. 131-139.
10.1016/j.sbi.2017.08.003.
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Varadi, Mihaly;
Nair, Sreenath;
Sillitoe, Ian;
Tauriello, Gerardo;
Anyango, Stephen;
Bienert, Stefan;
Borges, Clemente;
... Velankar, Sameer; + view all
(2022)
3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources.
Gigascience
, 11
, Article giac118. 10.1093/gigascience/giac118.
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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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Yachdav, G;
Wilzbach, S;
Rauscher, B;
Sheridan, R;
Sillitoe, I;
Procter, J;
Lewis, SE;
... Goldberg, T; + view all
(2016)
MSAViewer: interactive JavaScript visualization of multiple sequence alignments.
Bioinformatics
, 32
(22)
pp. 3501-3503.
10.1093/bioinformatics/btw474.
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Yeats, C;
Lees, J;
Carter, P;
Sillitoe, I;
Orengo, C;
(2011)
The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.
Nucleic Acids Research
, 39
W546-W550.
10.1093/nar/gkr438.
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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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