A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps

Authors:
Kamal Al Nasr;Lin Chen;Desh Ranjan;M. Zubair;Dong Si;Jing He
Affiliations:
Dept. of Computer Science, Tennessee State University, 3500 John A Merritt Blvd, Nashville, TN 37209;Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529;Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529;Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529;Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529;Dept. of Computer Science, Old Dominion University, Norfolk, VA 23529
Venue:
Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Year:
2013

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Abstract

Although many electron density maps have been produced into the medium resolutions, it is still challenging to derive the atomic structure from such volumetric data. Current methods primarily rely on the availability of an existing atomic structure for fitting or a homologous template structure for modeling. In the process of developing a template-free, de novo, method, the topology of the secondary structure elements need to be resolved first. In this paper, we extend our previous algorithm of finding the optimal solution in the constraint graph problem. We illustrate an approach to obtain the top-K topologies by combining a dynamic programming algorithm with the K-shortest path algorithm. The effectiveness of the algorithms is demonstrated from the test using three datasets of different nature. The algorithm improves the accuracy, space and time of an existing method.