Subsets of adjacent nodes (SOAN): a fast method for computing suboptimal paths in protein dynamic networks

Authors

Thomas Dodd, Georgia State University
Xin-Qiu Joe Yao, University of Nebraska at OmahaFollow
Donald Hamelberg, Georgia State UniversityFollow
Ivaylo Lvanov, Georgia State UniversityFollow

Author ORCID Identifier

Yao - https://orcid.org/0000-0003-2706-2028

Dodd - https://orcid.org/0000-0003-3149-013X

Hamelberg -https://orcid.org/0000-0002-3785-3037

Ivanov - https://orcid.org/0000-0002-5306-1005

Document Type

Article

Publication Date

3-4-2021

Publication Title

Molecular Physics

Volume

119

Issue

19-20

DOI

https://doi.org/10.1080/00268976.2021.1893847

Abstract

Suboptimal path analysis in a protein structural or dynamical network becomes increasingly popular for identifying critical residues involved in allosteric communication and regulation. Several software packages have been developed for calculating suboptimal paths, including NetworkView, WISP, and CNAPATH (Bio3D). Although these packages work well for biological systems of moderate sizes, they either dramatically slow down or are subjected to accuracy issues when applied to large systems such as supramolecular complexes. In this work, we develop a new method called SOAN, which implements a modified version of Yen’s algorithm for finding loopless k-shortest paths. Instead of searching the entire protein network, SOAN builds up a subgraph for path calculations based on an initial evaluation of the optimal path and its neighbouring nodes. We test our method on four systems of increasing size and compare it to the NetworkView, WISP and CNAPATH methods. The result shows that SOAN is approximately five times faster than NetworkView and orders of magnitude faster than CNAPATH and WISP. In terms of accuracy, SOAN is comparable to CNAPATH and WISP and superior to NetworkView. We also discuss the influence of SOAN input parameters on performance and suggest optimal values.

Comments

This is an Accepted Manuscript of an article published by Taylor & Francis in Molecular Physics on March 4, 2021, available online:

• https://doi.org/10.1080/00268976.2021.1893847

Recommended Citation

Dodd, T., Yao, X. Q., Hamelberg, D., & Ivanov, I. (2021). Subsets of adjacent nodes (SOAN): a fast method for computing suboptimal paths in protein dynamic networks. Molecular Physics, 119(19–20). https://doi.org/10.1080/00268976.2021.1893847

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 4.0 License.