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Biomedical subjects

D R Gilbert

Publications and source records attributed to D R Gilbert.

4 recordsLinked to original sources
PubMed2005

Protein structure topological comparison, discovery and matching service.

UNLABELLED: We describe a fold level fast protein comparison and motif matching facility based on the TOPS representation of structure. This provides an update to a previous service at the EBI, with a better graph matching with faster results and visualization of both the structures being compared against and the common pattern of each with the target domain. AVAILABILITY: Web service at http://balabio.dcs.gla.ac.uk/tops or via the main TOPS site at http://www.tops.leeds.ac.uk. Software is also available for download from these sites.

Algorithms↗
PubMed2003

Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing.

Topsalign is a method that will structurally align diverse protein structures, for example, structural alignment of protein superfolds. All proteins within a superfold share the same fold but often have very low sequence identity and different biological and biochemical functions. There is often significant structural diversity around the common scaffold of secondary structure elements of the fold. Topsalign uses topological descriptions of proteins. A pattern discovery algorithm identifies equivalent secondary structure elements between a set of proteins and these are used to produce an initial multiple structure alignment. Simulated annealing is used to optimize the alignment. The output of Topsalign is a multiple structure-based sequence alignment and a 3D superposition of the structures. This method has been tested on three superfolds: the beta jelly roll, TIM (alpha/beta) barrel and the OB fold. Topsalign outperforms established methods on very diverse structures. Despite the pattern discovery working only on beta strand secondary structure elements, Topsalign is shown to align TIM (alpha/beta) barrel superfamilies, which contain both alpha helices and beta strands.

Protein Structure, Secondary↗
PubMed2000

Interactive visualization and exploration of relationships between biological objects.

Genome sequencing and microarray technology produce ever-increasing amounts of complex data that need analysis. Visualization is an effective analytical technique that exploits the ability of the human brain to process large amounts of data. Here, we review traditional visualization methods based on clustering and tree representation, and also describe an alternative approach that involves projecting objects onto a Euclidean space in a way that reflects their structural or functional distances. Data are visualized without preclustering and can be dynamically explored by the user using 'virtual-reality'. We illustrate this approach with two case studies from protein topology and gene expression.

Biometry↗