@inproceedings{2c8bf32932bc4fa1898f5525b2008470,
title = "A constrained K-shortest path algorithm to rank the topologies of the protein secondary structure elements detected in CryoEM volume maps",
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.",
keywords = "Algorithm, Electron cryomicroscopy, Graph, K-shortest paths, Protein, Topology",
author = "{Al Nasr}, Kamal and Lin Chen and Desh Ranjan and M. Zubair and Dong Si and Jing He",
year = "2013",
doi = "10.1145/2506583.2506705",
language = "English (US)",
isbn = "9781450324342",
series = "2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013",
pages = "749--755",
booktitle = "2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013",
note = "2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 ; Conference date: 22-09-2013 Through 25-09-2013",
}