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Finding 3-D Similarities in
Protein Structures |
Finding similarities in the 3-dimesional structures of
proteins is not a trivial matter. See for example Godzik, Protein
Sci. 1996 5(7):1325-1338.
We have implemented two different methods for comparing
protein structures with different underlying assumptions:
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Combinatorial Extension
(CE) determines an optimal alignment between aligned fragment pairs (AFPs).
AFPs are determined from local geometry averaged over 8 C alpha positions.
Heuristics are used to prevent a combinatorial explosion.Final alignments
are by dynamic programming.
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Compound Likeness
(CL) uses a probabalistic approach to comparing a wide variety of properties.
Refer to each method for details.
This work is funded by the National Science Foundation.