Protein Engineering, Vol 11, 739-747, Copyright © 1998 by Oxford University Press
IN Shindyalov and PE Bourne
A new algorithm is reported which builds an alignment between two protein
structures. The algorithm involves a combinatorial extension (CE) of an
alignment path defined by aligned fragment pairs (AFPs) rather than the
more conventional techniques using dynamic programming and Monte Carlo
optimization. AFPs, as the name suggests, are pairs of fragments, one from
each protein, which confer structure similarity. AFPs are based on local
geometry, rather than global features such as orientation of secondary
structures and overall topology. Combinations of AFPs that represent
possible continuous alignment paths are selectively extended or discarded
thereby leading to a single optimal alignment. The algorithm is fast and
accurate in finding an optimal structure alignment and hence suitable for
database scanning and detailed analysis of large protein families. The
method has been tested and compared with results from Dali and VAST using a
representative sample of similar structures. Several new structural
similarities not detected by these other methods are reported. Specific
one-on-one alignments and searches against all structures as found in the
Protein Data Bank (PDB) can be performed via the Web at
http://cl.sdsc.edu/ce.html.
ARTICLES
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path
San Diego Supercomputer Center, CA 92186, USA.
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