Tony E. Lewis

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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 structural domains classified in CATH, up to 86 151 domains. Release 3.0 comprises 1110 fold groups and 2147 homologous superfamilies. To cope with the increases in diverse structural homologues being(More)
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(More)
The CATH database of protein domain structures (http://www.biochem.ucl.ac.uk/bsm/cath/) currently contains 43,229 domains classified into 1467 superfamilies and 5107 sequence families. Each structural family is expanded with sequence relatives from GenBank and completed genomes, using a variety of efficient sequence search protocols and reliable thresholds.(More)
The latest version of CATH (class, architecture, topology, homology) (version 3.2), released in July 2008 (http://www.cathdb.info), contains 114,215 domains, 2178 Homologous superfamilies and 1110 fold groups. We have assigned 20,330 new domains, 87 new homologous superfamilies and 26 new folds since CATH release version 3.1. A total of 28,064 new domains(More)
The latest version of the CATH-Gene3D protein structure classification database (4.0, http://www.cathdb.info) provides annotations for over 235,000 protein domain structures and includes 25 million domain predictions. This article provides an update on the major developments in the 2 years since the last publication in this journal including: significant(More)
CATH version 3.3 (class, architecture, topology, homology) contains 128,688 domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus on classifying structural genomics (SG) structures and transmembrane proteins, both of which are likely to add structural novelty to the database and therefore increase the coverage of protein(More)
This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved(More)
In this paper, we describe our work to investigate how much cyclic graph based Genetic Programming (GP) can be accelerated on one machine using currently available mid-range Graphics Processing Units (GPUs). Cyclic graphs pose different problems for evaluation than do trees and we describe how our CUDA based, "population parallel" evaluator tackles these(More)
If a population of programs evolved not for a few hundred generations but for a few hundred thousand or more, could it generate more interesting behaviours and tackle more complex problems? We begin to investigate this question by introducing Tweaking Mutation Behaviour Learning (TMBL), a form of evolutionary computation designed to meet this challenge.(More)
The most impressive accelerations of Genetic Programming (GP) using the Graphics Processing Unit (GPU) have been achieved by dynamically compiling new GPU code for each batch of individuals to be evaluated. This approach suffers an overhead in compilation time. We aim to reduce this penalty by pre-processing the individuals to identify and draw out their(More)