[Colloquium] Show and Tell Series at TTI-C (Xu on November 15th @ 12:15pm)

[Katherine Cumming]

TTI-C SHOW AND TELL SERIES
 
Presented by:  Toyota Technological Institute at Chicago
 
 
Speaker: Jinbo Xu, TTI-C
Speaker's home page: http://www.tti-c.org//jinbo_xu.html
 
Time: Tuesday, November 15th, 2005
Location: TTI-C Conference Room
Lunch Provided @ 12:00pm 
Seminar @ 12:15pm
 
Title: A Parameterized Algorithm for Protein Structure Alignment
 
Abstract:
 
I will present a parameterized algorithm for aligning two protein
structures, in the case where one protein structure is represented by a
contact map graph and the other by a contact map graph or a distance matrix.
If the sequential order of alignment is not required, the time complexity is
polynomial in the protein size and exponential with respect to several
parameters, which usually can be treated as constants. In particular, to
obtain an alignment with score at least $(1-\frac{1}{k})$ times optimal, the
running time of the parameterized algorithm is
$O(k^2poly(n)2^{tw\lg{\Delta}}/(\epsilon D_c)^6)$ where $poly(n)$ is a
polynomial in the protein size $n$,
$tw=O(k^2\frac{\max\{2D_c,D_u\}^3}{D_l^3})$, $\Delta=(1+\frac{2D_c}
{D_l})^3$, $\epsilon$ is a small positive number, $D_u$ is the distance
threshold determining if two residues are in contact or not, $D_c$ is the
maximally allowed distance between two matched residues after two proteins
are superimposed, and $D_l$ is the minimum inter-residue distance in a
typical protein. This result indicates that if both $\frac{D_u}{D_l}$ and
$\frac{D_c} {D_l}$ are small enough, then there is a polynomial-time
approximation scheme for the non-sequential protein structure alignment
problem. Empirically, both $\frac{D_u}{D_l}$ and $\frac{D_c}{D_l}$ are very
small and can be treated as constants.
 
The same algorithm can also be used for the structure alignment in the case
where the sequential order of alignment is enforced, although we do not have
such a good time complexity. This result clearly demonstrates that the
hardness of the contact-map based protein structure alignment problem is
related not to protein size but to several parameters, which depend on how
the protein structure alignment problem is modeled. The result is achieved
by decomposing the protein structure using tree decomposition and
discretizing the rigid-body transformation space. We have implemented our
algorithm and the preliminary experimental results indicate that on a Linux
PC, it takes from ten minutes to one hour to align two proteins with
approximately 100 residues.
 
This is a joint work with Feng Jiao (Waterloo) and Bonnie Berger (MIT). 
 
 
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If you have questions, or would like to meet the speaker, please contact
Katherine at 773-834-1994 or kcumming at tti-c.org.  For information on future
TTI-C talks or events, please go to the TTI-C Events page,
http://www.tti-c.org/events.html.  TTI-C (1427 East 60th Street, Chicago, IL
60637)
 
 
 
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