Lawrence A Kelley
Affiliation: Imperial College
- Discovering rules for protein-ligand specificity using support vector inductive logic programmingLawrence A Kelley
Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London, UK
Protein Eng Des Sel 22:561-7. 2009..The representation is sufficiently general to be applicable to any discriminatory binding problem. All programs and data sets are freely available to non-commercial users at http://www.sbg.bio.ic.ac.uk/svilp_ligand/...
- Protein structure prediction on the Web: a case study using the Phyre serverLawrence A Kelley
Structural Bioinformatics Group, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, South Kensington Campus, London, UK
Nat Protoc 4:363-71. 2009..Phyre is widely used by the biological community, with >150 submissions per day, and provides a simple interface to results. Phyre takes 30 min to predict the structure of a 250-residue protein...
- 3DLigandSite: predicting ligand-binding sites using similar structuresMark N Wass
Structural Bioinformatics Group, Centre for Bioinformatics, Imperial College London, London, SW7 2AZ, UK
Nucleic Acids Res 38:W469-73. 2010..68. The web server enables users to submit either a query sequence or structure. Predictions are visually displayed via an interactive Jmol applet. 3DLigandSite is available for use at http://www.sbg.bio.ic.ac.uk/3dligandsite...
- Sequencing delivers diminishing returns for homology detection: implications for mapping the protein universeDaniel Chubb
Department of Life Science, Imperial College London, London, UK
Bioinformatics 26:2664-71. 2010..The ability to discern such relationships is widely expected to grow as sequencing projects provide novel information, bridging gaps in our map of the protein universe...
- Exploring the extremes of sequence/structure space with ensemble fold recognition in the program PhyreRiccardo M Bennett-Lovsey
Structural Bioinformatics Group, Division of Molecular Biosciences, Imperial College London, London SW7 2AY, United Kingdom
Proteins 70:611-25. 2008..The results indicate greater coverage of sequence space and improved model quality, which can consequently lead to a reduction in the experimental workload of structural genomics initiatives...
- Protein folding requires crowd control in a simulated cellBenjamin R Jefferys
Division of Molecular Biosciences, Biochemistry Building, Imperial College London, South Kensington, London SW7 2AZ, UK
J Mol Biol 397:1329-38. 2010..Here, we discuss the possible implications regarding the relationship between protein expression level, protein size, chaperone activity and aggregation...
- Capturing expert knowledge with argumentation: a case study in bioinformaticsBenjamin R Jefferys
Division of Molecular Biosciences, Imperial College, London SW7 2AZ, UK
Bioinformatics 22:924-33. 2006..Often the process is laborious, goes unrecorded and may be biased. Argumentation is an established technique for reasoning about situations where absolute truth or precise probability is impossible to determine...
- Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domainsTony E Lewis
Institute of Structural and Molecular Biology, UCL, 636 Darwin Building, Gower Street, London, WC1E 6BT, UK
Nucleic Acids Res 41:D499-507. 2013..This has identified pairs of similar superfamilies from the two resources at various degrees of consensus (532 bronze pairs, 527 silver pairs and 370 gold pairs)...
- The proteome: structure, function and evolutionKeiran Fleming
Structural Bioinformatics Group, Centre for Bioinformatics, Division of Molecular Biosciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK
Philos Trans R Soc Lond B Biol Sci 361:441-51. 2006..The method is also able to identify the specific residues associated with the function of the protein family...
- A new structural model of the acid-labile subunit: pathogenetic mechanisms of short stature-causing mutationsAlessia David
Centre for Integrative Systems Biology and Bioinformatics, Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
J Mol Endocrinol 49:213-20. 2012..The new model allowed us to analyse the ALS core and its caps and to interpret the potential structural effects of ALS mutations...
- The extent and importance of intragenic recombinationEric de Silva
Department of Biological Sciences, Imperial College London, Wolfson Building, South Kensington Campus, London SW7 2AZ, UK
Hum Genomics 1:410-20. 2004..This suggests that evolutionary analysis of the recombination process is greatly aided by considering nucleotide sequences and protein products jointly...