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Protein fold recognition from secondary structure assignments

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3 Author(s)
R. B. Russell ; Lab. of Molecular Biophys., Oxford, UK ; R. R. Copley ; G. J. Barton

A method for finding protein folds consistent with secondary structure assignments and imposed experimental restraints is described. All possible matches between the query pattern and every member of a database of protein structural domains are generated by a comparison of secondary structure assignments. The comparison allows for errors in predicted secondary structure elements and possible variations between query and database structure. Several filters remove matches that are un-compact, that have poor β sheet bonding, that do not allow loop/turn lengths to bridge the distance between connected secondary structures, or that fail to satisfy imposed experimental restraints (e.g. disulphide bonds). The remaining matches provide a set of plausible topologies for a protein of unknown structure, which can be inspected visually or tested by experiment. A search using the src homology 2 domain prediction finds 13 possible topologies, one being a domain from the E. coli bio protein known to adopt an SH2 fold. The use and development of the method are discussed

Published in:

System Sciences, 1995. Proceedings of the Twenty-Eighth Hawaii International Conference on  (Volume:5 )

Date of Conference:

3-6 Jan 1995