A constrained K-shortest path algorithm to rank the topologies of the protein secondary structure elements detected in CryoEM volume maps

Kamal Al Nasr, Lin Chen, Desh Ranjan, M. Zubair, Dong Si, Jing He

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

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.

Original languageEnglish (US)
Title of host publication2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Pages749-755
Number of pages7
DOIs
StatePublished - 2013
Externally publishedYes
Event2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013 - Wshington, DC, United States
Duration: Sep 22 2013Sep 25 2013

Publication series

Name2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013

Conference

Conference2013 4th ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics, ACM-BCB 2013
Country/TerritoryUnited States
CityWshington, DC
Period9/22/139/25/13

Keywords

  • Algorithm
  • Electron cryomicroscopy
  • Graph
  • K-shortest paths
  • Protein
  • Topology

ASJC Scopus subject areas

  • Bioengineering
  • Biomedical Engineering
  • Health Informatics

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