Document Type

Article

Publication Date

2015

DOI

10.1089/cmb.2015.0120

Publication Title

Journal of Computational Biology

Volume

22

Issue

9

Pages

837-843

Abstract

The determination of secondary structure topology is a critical step in deriving the atomic structures from the protein density maps obtained from electron cryomicroscopy technique. This step often relies on matching the secondary structure traces detected from the protein density map to the secondary structure sequence segments predicted from the amino acid sequence. Due to inaccuracies in both sources of information, a pool of possible secondary structure positions needs to be sampled. One way to approach the problem is to first derive a small number of possible topologies using existing matching algorithms, and then find the optimal placement for each possible topology. We present a dynamic programming method of Θ(Nq2h) to find the optimal placement for a secondary structure topology. We show that our algorithm requires significantly less computational time than the brute force method that is in the order of Θ(qN h).

Rights

© 2015 Mary Ann Liebert, Inc. All rights reserved.

Included in accordance with publisher policy.

Original Publication Citation

Biswas, A., Ranjan, D., Zubair, M., & He, J. (2015). A dynamic programming algorithm for finding the optimal placement of a secondary structure topology in Cryo-EM data. Journal of Computational Biology, 22(9), 837-843. https://doi.org/10.1089/cmb.2015.0120

ORCID

0000-0002-8074-2543 (Biswas), 0000-0002-5449-1779 (Zubair)

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