TOPS

  • a system for visualization, database searching, comparison and machine learning of protein structural topology. The project has created a database of protein protein topology, enhanced with sequence and function-related information. Fast and efficient algorithms have been developed for structure comparison, motif discovery and pattern matching, and versions are being developed to include sequence and function information. Visualization facilities for TOPS diagrams have also been developed. The most speculative part of the project, is the investigation of machine learning for structure-sequence-function relationships, which aims to learn patterns linking topology to sequence, and topology and sequence to function. Interesting results will be valuable to efforts to predict protein structure and function from sequences, and these problems remain key challenges of direct relevance to projects in structural and functional genomics.

Developers

David Westhead

David Brunel

Categories

Structure Analysis

Versions

Citations

Westhead et al. Protein structural topology: automated analysis, diagrammatic representation and database searching. Protein Sci. 1999. 8(4):897-904.

Gilbert. Motif-based searching in TOPS protein topology databases. Bioinformatics. 1999. 15(4):317-26.

License Type

This software is distributed under an Open license.

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