Assignment of Protein Secondary Structure Elements from Cα Backbone Trace: An Ensemble of Machine Learning Approaches

Kamal Al Nasr, Ali Sekmen

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

Abstract

Secondary structure elements in protein molecules refer to local sub-conformational regions stabilized by hydrogen bonding. Assigning Secondary Structure Elements is crucial in protein structure determination and function analysis. This work represents a recast of a previously developed classifier using ensemble of machine learning models. In this paper, we introduce new geometrical features to improve the accuracy, reduce training data set and process, and we develop and apply a post-processing step. The classifier is trained with 150K amino acids. We tested our classifier on a set of 20 protein structures and compared with previously developed classifier. The information from Protein Data Bank was used as a reference. The comparison shows that new method can produce assignments that are more aligned with PDB at 95.31% accuracy after applying a simple postprocessing step compared to 92.75% for the previous classifier.

Original languageEnglish (US)
Title of host publicationProceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021
EditorsYufei Huang, Lukasz Kurgan, Feng Luo, Xiaohua Tony Hu, Yidong Chen, Edward Dougherty, Andrzej Kloczkowski, Yaohang Li
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages2541-2545
Number of pages5
ISBN (Electronic)9781665401265
DOIs
StatePublished - 2021
Externally publishedYes
Event2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021 - Virtual, Online, United States
Duration: Dec 9 2021Dec 12 2021

Publication series

NameProceedings - 2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021

Conference

Conference2021 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2021
Country/TerritoryUnited States
CityVirtual, Online
Period12/9/2112/12/21

Keywords

  • Cα Backbone Trace
  • Machine Learning
  • Protein Modeling
  • Secondary Structure Assignment

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Science Applications
  • Biomedical Engineering
  • Health Informatics
  • Information Systems and Management

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