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Fast Pairwise Alignment of Protein Structures Based on Conformational Letters
Speaker:
Prof. Wei-Mou Zheng
Institute of Theoretical Physics, Chinese Academy of Sciences
Time: 2:00-3:00pm, Friday October 19
Location: Room 610, New Life Science Building, Peking University
Fast, efficient and reliable algorithms for pairwise alignment
of protein structures are in ever increasing demand for analyzing
the rapidly growing data of protein structures. CLePAPS is a tool
developed for this purpose. It distinguishes itself from other
existing algorithms by the use of conformational letters, which
are discretized states of 3D segmental structural states. A letter
corresponds to a cluster of combinations of the three angles formed
by C-alpha pseudobonds of four contiguous residues. A substitution
matrix called CLESUM is available to measure similarity between any
two such letters. CLePAPS regards a similar fragment pair (SFP) as
an ungapped string pair with a high sum of pairwise CLESUM scores.
Using CLESUM scores as the similarity measure, CLePAPS searches for
SFPs by simple string comparison. The transformation which best
superimposes a highly similar SFP can be used to superimpose the
structure pairs under comparison. A highly scored SFP which is
consistent with several other SFPs determines an initial alignment.
CLePAPS then joins consistent SFPs guided by their similarity scores
to extend the alignment by several `zoom-in' iteration steps. A
follow-up refinement produces the final alignment. CLePAPS does not
implement dynamic programming. The utility of CLePAPS has been tested
on various protein structure pairs.
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