Gaps and PAMs

David T Jones ucbcdtj at ucl.ac.uk
Mon Jun 29 16:45:12 EST 1992

In my last posting I mentioned the term 'structural alignment' which
I now realize may not be familiar to everyone. I was referring to methods
which actually align protein structures rather than sequences. This
is somewhat akin to superposing two protein structures in order to
identify topologically equivalent residues in the protein cores. The
difference between superposition and structural alignment is that
as with sequence alignment, structural alignment actually allows for
insertions and deletions in the structures.

The actual method I use was developed by W.R. Taylor and C.A. Orengo -
see the following ref. for details:

Orengo C.A. and Taylor W.R. J. theor. Biol. 147:517-551 (1990).

David Jones
University College London

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