Speaker:
Yonggang Lu (PhD student at NMSU, advisor Dr. Jing He)


Title: An Algorithm for Helices Mapping between 3D and
1D Protein Structure

Abstract: 
3-dimensional (3D) structure determination of proteins is a 
challenging problem, especially for large protein complexes 
and membrane proteins. We designed an algorithm for building
a library to map helices in a 3D structure to its 1-dimensional
(1D) structure, by using the length constraints of helices.
The parallel version of the program used a full decentralized 
scheduling strategy and it got a near linear speedup of the excution
time. Depth-first search is used to decrease the memory usage.
Because of the exponential nature of the problem, we constructed 
a library of more likely mappings rather than generating a complete 
mapping library. The results indicate that our method is able to 
work with small to medium-sized proteins. If the secondary structure
prediction is good, our method is able to contain a mapping that 
correctly assigns the majority of the helices.