Benoit H. Dessailly
University College London
Binding siteData miningFunction (biology)GenomeProtein domainDomain (software engineering)GenomicsStructural genomicsMolecular Sequence AnnotationFunctional diversityComputer scienceSequence alignmentStructural alignmentProtein structureGeneticsBiochemistryStructural Classification of Proteins databaseBioinformaticsComputational biologyBiologyProtein Structure InitiativeSUPERFAMILY
26Publications
18H-index
1,289Citations
Publications 25
Newest
#1Sergio Picart-Armada (UPC: Polytechnic University of Catalonia)H-Index: 5
#2Steven J. BarrettH-Index: 1
Last. Benoit H. DessaillyH-Index: 18
view all 6 authors...
In-silico identification of potential target genes for disease is an essential aspect of drug target discovery. Recent studies suggest that successful targets can be found through by leveraging genetic, genomic and protein interaction information. Here, we systematically tested the ability of 12 varied algorithms, based on network propagation, to identify genes that have been targeted by any drug, on gene-disease data from 22 common non-cancerous diseases in OpenTargets. We considered two biolog...
19 CitationsSource
#1Yi-An ChenH-Index: 9
#2Lokesh P. TripathiH-Index: 12
Last. Kenji MizuguchiH-Index: 38
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Prioritising candidate genes for further experimental characterisation is an essential, yet challenging task in biomedical research. One way of achieving this goal is to identify specific biological themes that are enriched within the gene set of interest to obtain insights into the biological phenomena under study. Biological pathway data have been particularly useful in identifying functional associations of genes and/or gene sets. However, biological pathway information as compiled in varied ...
22 CitationsSource
#1Jonathan G. Lees (UCL: University College London)H-Index: 26
#2David A. Lee (UCL: University College London)H-Index: 71
Last. Christine A. Orengo (UCL: University College London)H-Index: 84
view all 10 authors...
Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of protein domain structure annotations for protein sequences. Domains are predicted using a library of profile HMMs from 2738 CATH superfamilies. Gene3D assigns domain annotations to Ensembl and UniProt sequence sets including >6000 cellular genomes and >20 million unique protein sequences. This represents an increase of 45% in the number of protein sequences since our last publication. Thanks to improvements in the underlying data and pipe...
40 CitationsSource
#1Corin Yeats (UCL: University College London)H-Index: 28
#2Benoit H. Dessailly (UCL: University College London)H-Index: 18
Last. Christine A. Orengo (UCL: University College London)H-Index: 84
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This chapter describes the protocols used to identify, filter, and annotate potential protein targets from an organism associated with infectious diseases. Protocols often combine computational approaches for mining information in public databases or for checking whether the protein has already been targeted for structure determination, with manual strategies that examine the literature for information on the biological role of the protein or the experimental strategies that explore the effects ...
1 CitationsSource
#1Benoit H. DessaillyH-Index: 18
#2Christine A. Orengo (UCL: University College London)H-Index: 84
Source
#1Benoit H. DessaillyH-Index: 18
#2Natalie L. Dawson (UCL: University College London)H-Index: 19
Last. Christine A. Orengo (UCL: University College London)H-Index: 84
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We present, to our knowledge, the first quantitative analysis of functional site diversity in homologous domain superfamilies. Different types of functional sites are considered separately. Our results show that most diverse superfamilies are very plastic in terms of the spatial location of their functional sites. This is especially true for protein–protein interfaces. In contrast, we confirm that catalytic sites typically occupy only a very small number of topological locations. Small-ligand bi...
26 CitationsSource
#1Choon Kit TangH-Index: 2
#2Taiki Aoshi (Osaka University)H-Index: 28
Last. Ken Ishii (Osaka University)H-Index: 96
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5,6-Dimethylxanthenone-4-acetic acid (DMXAA), a potent type I interferon (IFN) inducer, was evaluated as a chemotherapeutic agent in mouse cancer models and proved to be well tolerated in human cancer clinical trials. Despite its multiple biological functions, DMXAA has not been fully characterized for the potential application as a vaccine adjuvant. In this report, we show that DMXAA does act as an adjuvant due to its unique property as a soluble innate immune activator. Using OVA as a model an...
21 CitationsSource
#1Björn Brindefalk (Stockholm University)H-Index: 6
#2Benoit H. Dessailly (Cant.: University of Canterbury)H-Index: 18
Last. Anthony M. Poole (Cant.: University of Canterbury)H-Index: 31
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The TATA binding protein (TBP) is an essential transcription initiation factor in Archaea and Eucarya. Bacteria lack TBP, and instead use sigma factors for transcription initiation. TBP has a symmetric structure comprising two repeated TBP domains. Using sequence, structural and phylogenetic analyses, we examine the distribution and evolutionary history of the TBP domain, a member of the helix-grip fold family. Our analyses reveal a broader distribution than for TBP, with TBP-domains being prese...
19 CitationsSource
#1Romain A. Studer (UCL: University College London)H-Index: 18
#2Benoit H. DessaillyH-Index: 18
Last. Christine A. Orengo (UCL: University College London)H-Index: 84
view all 3 authors...
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 the law of natural selection and undergo alternating periods of conservative evolution and of relatively rapid change. The likelihood of mutations being fixed in the genome depends on various factors, such as the fitness of the phenotype or the position of the residues in the three-dimensional structure. For example, co-evolution of resid...
151 CitationsSource
#1Ian Sillitoe (EMBL-EBI: European Bioinformatics Institute)H-Index: 33
#2Alison L. Cuff (EMBL-EBI: European Bioinformatics Institute)H-Index: 13
Last. Christine A. Orengo (EMBL-EBI: European Bioinformatics Institute)H-Index: 84
view all 13 authors...
CATH version 3.5 (Class, Architecture, Topology, Homology, available at http://www.cathdb.info/) contains 173 536 domains, 2626 homologous superfamilies and 1313 fold groups. When focusing on structural genomics (SG) structures, we observe that the number of new folds for CATH v3.5 is slightly less than for previous releases, and this observation suggests that we may now know the majority of folds that are easily accessible to structure determination. We have improved the accuracy of our functio...
186 CitationsSource