A graph-based algorithm for detecting rigid domains in protein structures

BMC Bioinformatics

Mehmet Gültas¹  Thach Nguyen²  Michael Habeck³  Stephan Waack⁴  Truong Khanh Linh Dang⁴ 

[1] Breeding Informatics Group, Department of Animal Sciences, Margarethe von Wrangell-Weg 7, 37075, Göttingen, Germany;Center for Integrated Breeding Research (CiBreed), Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany;Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Goldschmidtstr 7, 37077, Göttingen, Germany;Felix Bernstein Institute for Mathematical Statistics in the Biosciences, University of Göttingen, Goldschmidtstr 7, 37077, Göttingen, Germany;Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany;Microscopic Image Analysis Group, University Hospital Jena, Am Klinikum 1, 07747, Jena, Germany;Institute of Computer Science, University of Göttingen, Goldschmidtstr 7, 37077, Göttingen, Germany;

关键词: Protein structural transition;    Graph algorithms;    Generalized Viterbi algorithm;   

DOI  :  10.1186/s12859-021-03966-3

来源: Springer

【 摘 要 】

BackgroundConformational transitions are implicated in the biological function of many proteins. Structural changes in proteins can be described approximately as the relative movement of rigid domains against each other. Despite previous efforts, there is a need to develop new domain segmentation algorithms that are capable of analysing the entire structure database efficiently and do not require the choice of protein-dependent tuning parameters such as the number of rigid domains.ResultsWe develop a graph-based method for detecting rigid domains in proteins. Structural information from multiple conformational states is represented by a graph whose nodes correspond to amino acids. Graph clustering algorithms allow us to reduce the graph and run the Viterbi algorithm on the associated line graph to obtain a segmentation of the input structures into rigid domains. In contrast to many alternative methods, our approach does not require knowledge about the number of rigid domains. Moreover, we identified default values for the algorithmic parameters that are suitable for a large number of conformational ensembles. We test our algorithm on examples from the DynDom database and illustrate our method on various challenging systems whose structural transitions have been studied extensively.ConclusionsThe results strongly suggest that our graph-based algorithm forms a novel framework to characterize structural transitions in proteins via detecting their rigid domains. The web server is available at http://azifi.tz.agrar.uni-goettingen.de/webservice/.

【 授权许可】

CC BY