Bioinformatics Vol. 16 no. 12 2000
Pages 1111-1119
© 2000 Oxford University Press
Original Paper |
Analysis of conservation and substitutions of secondary structure elements within protein superfamilies
Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrookes Site, Cambridge CB2 1GA, UK
Received on May 30, 2000
; revised on June 30, 2000
; accepted on July 25, 2000
Motivation: Structural alignments of superfamily members often exhibit insertions and deletions of secondary structure elements (SSEs), yet conserved subsets of SSEs appear to be important for maintaining the fold and facilitating common functionalities.
Results: A database of aligned SSEs was constructed from the structure-based alignments of protein superfamily members in the CAMPASS database. SSEs were classified into several types on the basis of their length and solvent accessibility and counts were made for the replacements of SSEs in different types at structurally aligned positions. The results, summarized as log-odds substitution matrices, can be used for two types of comparisons: (1) structure against structure, both with secondary structure assignments; and (2) structure against sequence with predicted secondary structures. The conservation of SSEs at each alignment position was defined as the deviation of observed SSE frequencies from the uniform distribution. This offers a useful resource to define and examine the core of superfamily folds. Even when the structure of only a single member of a superfamily is known, the extended method can be used to predict the conservation of SSEs. Such information will be useful when modelling the structure of other members of a superfamily or identifying structurally and functionally important positions in the fold.
Availability: The database is available on the world wide web at http://www-cryst.bioc.cam.ac.uk/~kenji/ssdb/. The conservation of SSEs was translated into colour values and can be visualized through the web interface.
Contact: kenji{at}cryst.bioc.cam.ac.uk
* To whom correspondence should be addressed.
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