Search Results - "Cuff, Alison"

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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Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies by Furnham, Nicholas, Sillitoe, Ian, Holliday, Gemma L, Cuff, Alison L, Laskowski, Roman A, Orengo, Christine A, Thornton, Janet M

“…In order to understand the evolution of enzyme reactions and to gain an overview of biological catalysis we have combined sequence and structural data to…”
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CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies by Cuff, Alison L, Sillitoe, Ian, Lewis, Tony, Redfern, Oliver C, Garratt, Richard, Thornton, Janet, Orengo, Christine A

“…The latest version of CATH (class, architecture, topology, homology) (version 3.2), released in July 2008 (http://www.cathdb.info), contains 1 14 215 domains,…”
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Extending CATH: increasing coverage of the protein structure universe and linking structure with function by Cuff, Alison L, Sillitoe, Ian, Lewis, Tony, Clegg, Andrew B, Rentzsch, Robert, Furnham, Nicholas, Pellegrini-Calace, Marialuisa, Jones, David, Thornton, Janet, Orengo, Christine A

“…CATH version 3.3 (class, architecture, topology, homology) contains 128 688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major…”
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Seventh BMC ecology image competition: the winning images by Cuff, Alison L, Baguette, Michel, Blanchet, Simon, Jacobus, Luke M, Mazzi, Dominique, Settele, Josef

“…Abstract The seventh BMC Ecology competition attracted entries from talented ecologists from around the world. Together, they showcase the beauty and diversity…”
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BMC ecology image competition 2018: the winning images by Cuff, Alison L, Lou, Ying, Zhigang, Jiang, Baguette, Michel, Blanchet, Simon, Clobert, Jean, Jacobus, Luke M, Mazzi, Dominique, Settele, Josef

“…The sixth BMC Ecology Image Competition received more than 145 photographs from talented ecologists around the world, showcasing the amazing biodiversity,…”
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Inaugural BMC Ecology and Evolution image competition: the winning images by Harman, Jennifer L., Cuff, Alison L., Settele, Josef, Jacobus, Luke M., Liberles, David A., Traulsen, Arne

“…Abstract The inaugural  BMC Ecology and Evolution  image competition attracted entries from talented ecologists and evolutionary biologists worldwide…”
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FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies by Furnham, Nicholas, Sillitoe, Ian, Holliday, Gemma L., Cuff, Alison L., Rahman, Syed A., Laskowski, Roman A., Orengo, Christine A., Thornton, Janet M.

“…FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme…”
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Correction to: Inaugural BMC Ecology and Evolution image competition: the winning images by Harman, Jennifer L, Cuff, Alison L, Settele, Josef, Jacobus, Luke M, Liberles, David A, Traulsen, Arne

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Detailed Analysis of Function Divergence in a Large and Diverse Domain Superfamily: Toward a Refined Protocol of Function Classification by Dessailly, Benoit H., Redfern, Oliver C., Cuff, Alison L., Orengo, Christine A.

“…Some superfamilies contain large numbers of protein domains with very different functions. The ability to refine the functional classification of domains…”
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Exploiting structural classifications for function prediction: towards a domain grammar for protein function by Dessailly, Benoît H, Redfern, Oliver C, Cuff, Alison, Orengo, Christine A

“…The ability to assign function to proteins has become a major bottleneck for comprehensively understanding cellular mechanisms at the molecular level. Here we…”
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Analysis of Void Volumes in Proteins and Application to Stability of the p53 Tumour Suppressor Protein by Cuff, Alison L., Martin, Andrew C.R.

“…We have developed a new method for the analysis of voids in proteins (defined as empty cavities not accessible to solvent). This method combines analysis of…”
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Integrating mutation data and structural analysis of the TP53 tumor-suppressor protein by Martin, Andrew C.R., Facchiano, Angelo M., Cuff, Alison L., Hernandez-Boussard, Tina, Olivier, Magali, Hainaut, Pierre, Thornton, Janet M.

“…TP53 encodes p53, which is a nuclear phosphoprotein with cancer‐inhibiting properties. In response to DNA damage, p53 is activated and mediates a set of…”
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The evolution of digital health and its continuing challenges by Cuff, Alison

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Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins by Cuff, Alison L., Janes, Robert W., Martin, Andrew C.R.

“…Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses…”
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Overcoming protein denaturation caused by irradiation in a high-flux synchrotron radiation circular dichroism beamline by Janes, Robert W, Cuff, Alison L

“…It has been established that the new circular dichroism beamline CD12 has sufficiently high flux at low wavelengths to cause apparent irradiation problems with…”
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CATH: comprehensive structural and functional annotations for genome sequences by Sillitoe, Ian, Lewis, Tony E, Cuff, Alison, Das, Sayoni, Ashford, Paul, Dawson, Natalie L, Furnham, Nicholas, Laskowski, Roman A, Lee, David, Lees, Jonathan G, Lehtinen, Sonja, Studer, Romain A, Thornton, Janet, Orengo, Christine A

“…The latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations for over 235,000 protein…”
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The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution by Greene, Lesley H, Lewis, Tony E, Addou, Sarah, Cuff, Alison, Dallman, Tim, Dibley, Mark, Redfern, Oliver, Pearl, Frances, Nambudiry, Rekha, Reid, Adam, Sillitoe, Ian, Yeats, Corin, Thornton, Janet M, Orengo, Christine A

“…We report the latest release (version 3.0) of the CATH protein domain database (http://www.cathdb.info). There has been a 20% increase in the number of…”
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The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution by Greene, Lesley H., Lewis, Tony E., Addou, Sarah, Cuff, Alison, Dallman, Tim, Dibley, Mark, Redfern, Oliver, Pearl, Frances, Nambudiry, Rekha, Reid, Adam, Sillitoe, Ian, Yeats, Corin, Thornton, Janet M., Orengo, Christine A.

“…We report the latest release (version 3.0) of the CATH protein domain database (). There has been a 20% increase in the number of structural domains classified…”
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Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains by Lewis, Tony E, Sillitoe, Ian, Andreeva, Antonina, Blundell, Tom L, Buchan, Daniel W A, Chothia, Cyrus, Cuff, Alison, Dana, Jose M, Filippis, Ioannis, Gough, Julian, Hunter, Sarah, Jones, David T, Kelley, Lawrence A, Kleywegt, Gerard J, Minneci, Federico, Mitchell, Alex, Murzin, Alexey G, Ochoa-Montaño, Bernardo, Rackham, Owen J L, Smith, James, Sternberg, Michael J E, Velankar, Sameer, Yeats, Corin, Orengo, Christine

“…Genome3D, available at http://www.genome3d.eu, is a new collaborative project that integrates UK-based structural resources to provide a unique perspective on…”
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