Search Results - "Orengo, Christine A."

InterPro in 2022 by Paysan-Lafosse, Typhaine, Blum, Matthias, Chuguransky, Sara, Grego, Tiago, Pinto, Beatriz Lázaro, Salazar, Gustavo A, Bileschi, Maxwell L, Bork, Peer, Bridge, Alan, Colwell, Lucy, Gough, Julian, Haft, Daniel H, Letunić, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, Sigrist, Christian J A, Sillitoe, Ian, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex

“…The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally…”
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CATH: increased structural coverage of functional space by Sillitoe, Ian, Bordin, Nicola, Dawson, Natalie, Waman, Vaishali P, Ashford, Paul, Scholes, Harry M, Pang, Camilla S M, Woodridge, Laurel, Rauer, Clemens, Sen, Neeladri, Abbasian, Mahnaz, Le Cornu, Sean, Lam, Su Datt, Berka, Karel, Varekova, Ivana Hutařová, Svobodova, Radka, Lees, Jon, Orengo, Christine A

“…Abstract CATH (https://www.cathdb.info) identifies domains in protein structures from wwPDB and classifies these into evolutionary superfamilies, thereby…”
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The InterPro protein families and domains database: 20 years on by Blum, Matthias, Chang, Hsin-Yu, Chuguransky, Sara, Grego, Tiago, Kandasaamy, Swaathi, Mitchell, Alex, Nuka, Gift, Paysan-Lafosse, Typhaine, Qureshi, Matloob, Raj, Shriya, Richardson, Lorna, Salazar, Gustavo A, Williams, Lowri, Bork, Peer, Bridge, Alan, Gough, Julian, Haft, Daniel H, Letunic, Ivica, Marchler-Bauer, Aron, Mi, Huaiyu, Natale, Darren A, Necci, Marco, Orengo, Christine A, Pandurangan, Arun P, Rivoire, Catherine, Sigrist, Christian J A, Sillitoe, Ian, Thanki, Narmada, Thomas, Paul D, Tosatto, Silvio C E, Wu, Cathy H, Bateman, Alex, Finn, Robert D

“…Abstract The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies…”
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CATH: an expanded resource to predict protein function through structure and sequence by Dawson, Natalie L, Lewis, Tony E, Das, Sayoni, Lees, Jonathan G, Lee, David, Ashford, Paul, Orengo, Christine A, Sillitoe, Ian

“…The latest version of the CATH-Gene3D protein structure classification database has recently been released (version 4.1, http://www.cathdb.info). The resource…”
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VarSite: Disease variants and protein structure by Laskowski, Roman A., Stephenson, James D., Sillitoe, Ian, Orengo, Christine A., Thornton, Janet M.

“…VarSite is a web server mapping known disease‐associated variants from UniProt and ClinVar, together with natural variants from gnomAD, onto protein 3D…”
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Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes by Studer, Romain A, Dessailly, Benoit H, Orengo, Christine A

“…The present review focuses on the evolution of proteins and the impact of amino acid mutations on function from a structural perspective. Proteins evolve under…”
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Computational approaches to predict protein functional families and functional sites by Rauer, Clemens, Sen, Neeladri, Waman, Vaishali P., Abbasian, Mahnaz, Orengo, Christine A.

“…Understanding the mechanisms of protein function is indispensable for many biological applications, such as protein engineering and drug design. However,…”
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Stability-activity tradeoffs constrain the adaptive evolution of RubisCO by Studer, Romain A., Christin, Pascal-Antoine, Williams, Mark A., Orengo, Christine A.

“…A well-known case of evolutionary adaptation is that of ribulose-1,5-bisphosphate carboxylase (RubisCO), the enzyme responsible for fixation of CO ₂ during…”
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CATH: expanding the horizons of structure-based functional annotations for genome sequences by Sillitoe, Ian, Dawson, Natalie, Lewis, Tony E, Das, Sayoni, Lees, Jonathan G, Ashford, Paul, Tolulope, Adeyelu, Scholes, Harry M, Senatorov, Ilya, Bujan, Andra, Ceballos Rodriguez-Conde, Fatima, Dowling, Benjamin, Thornton, Janet, Orengo, Christine A

“…Abstract This article provides an update of the latest data and developments within the CATH protein structure classification database…”
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Protein function prediction using domain families by Rentzsch, Robert, Orengo, Christine A

“…Here we assessed the use of domain families for predicting the functions of whole proteins. These 'functional families' (FunFams) were derived using a protocol…”
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Functional classification of CATH superfamilies: a domain-based approach for protein function annotation by Das, Sayoni, Lee, David, Sillitoe, Ian, Dawson, Natalie L, Lees, Jonathan G, Orengo, Christine A

“…Computational approaches that can predict protein functions are essential to bridge the widening function annotation gap especially since <1.0% of all proteins…”
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Protein function annotation using protein domain family resources by Das, Sayoni, Orengo, Christine A.

“…•Homology based predictions from protein families perform well.•Functional classification of protein families increase accuracy of function…”
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Biological impact of mutually exclusive exon switching by Lam, Su Datt, Babu, M Madan, Lees, Jonathan, Orengo, Christine A

“…Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in…”
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New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures by Sillitoe, Ian, Cuff, Alison L, Dessailly, Benoit H, Dawson, Natalie L, Furnham, Nicholas, Lee, David, Lees, Jonathan G, Lewis, Tony E, Studer, Romain A, Rentzsch, Robert, Yeats, Corin, Thornton, Janet M, Orengo, Christine A

“…CATH version 3.5 (Class, Architecture, Topology, Homology, available at http://www.cathdb.info/) contains 173 536 domains, 2626 homologous superfamilies and…”
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Predicting human and viral protein variants affecting COVID-19 susceptibility and repurposing therapeutics by Waman, Vaishali P., Ashford, Paul, Lam, Su Datt, Sen, Neeladri, Abbasian, Mahnaz, Woodridge, Laurel, Goldtzvik, Yonathan, Bordin, Nicola, Wu, Jiaxin, Sillitoe, Ian, Orengo, Christine A.

“…The COVID-19 disease is an ongoing global health concern. Although vaccination provides some protection, people are still susceptible to re-infection…”
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Protein function prediction – the power of multiplicity by Rentzsch, Robert, Orengo, Christine A

“…Advances in experimental and computational methods have quietly ushered in a new era in protein function annotation. This ‘age of multiplicity’ is marked by…”
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Gene3D: expanding the utility of domain assignments by Lam, Su Datt, Dawson, Natalie L, Das, Sayoni, Sillitoe, Ian, Ashford, Paul, Lee, David, Lehtinen, Sonja, Orengo, Christine A, Lees, Jonathan G

“…Gene3D http://gene3d.biochem.ucl.ac.uk is a database of domain annotations of Ensembl and UniProtKB protein sequences. Domains are predicted using a library of…”
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Low-Density Lipoprotein Receptor Gene Familial Hypercholesterolemia Variant Database: Update and Pathological Assessment by Usifo, Ebele, Leigh, Sarah E. A., Whittall, Ros A., Lench, Nicholas, Taylor, Alison, Yeats, Corin, Orengo, Christine A., Martin, Andrew C. R., Celli, Jacopo, Humphries, Steve E.

“…Summary Familial hypercholesterolemia (FH) is caused predominately by variants in the low‐density lipoprotein receptor gene (LDLR). We report here an update of…”
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Exploring the structure and function paradigm by Redfern, Oliver C., Dessailly, Benoit, Orengo, Christine A.

“…Advances in protein structure determination, led by the structural genomics initiatives have increased the proportion of novel folds deposited in the Protein…”
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Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster by Wan, Cen, Lees, Jonathan G, Minneci, Federico, Orengo, Christine A, Jones, David T

“…Accurate gene or protein function prediction is a key challenge in the post-genome era. Most current methods perform well on molecular function prediction, but…”
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