loading page

A new method for protein characterization and classification using geometrical features for 3D face analysis: an example of tubulin structures
  • +3
  • Luca di Grazia,
  • Maral Aminpour,
  • Enrico Vezzetti,
  • Vahid Rezania,
  • Federica Marcolin,
  • Jack Tuszynski
Luca di Grazia
Politecnico di Torino
Author Profile
Maral Aminpour
University of Alberta, University of Alberta
Author Profile
Enrico Vezzetti
Politecnico di Torino
Author Profile
Vahid Rezania
MacEwan University City Centre Campus
Author Profile
Federica Marcolin
Politecnico di Torino
Author Profile
Jack Tuszynski
University of Alberta
Author Profile

Abstract

This paper reports on the results of research aimed to translate biometric 3D face recognition concepts and algorithms into the field of protein biophysics in order to precisely and rapidly classify morphological features of protein surfaces. Both human faces and protein surfaces are free-forms and some descriptors used in differential geometry can be used to describe them applying the principles of feature extraction developed for computer vision and pattern recognition. The first part of this study focused on building the protein dataset using a simulation tool and performing feature extraction using novel geometrical descriptors. The second part tested the method on two examples, first involved a classification of tubulin isotypes and the second compared tubulin with the FtSZ protein, which is its bacterial analogue. An additional test involved several unrelated proteins. Different classification methodologies have been used: a classic approach with a Support Vector Machine (SVM) classifier and an unsupervised learning with a k-means approach. The best result was obtained with SVM and the radial basis function (RBF) kernel. The results are significant and competitive with the state-of-the-art protein classification methods. This opens a new area for protein structure analysis.

Peer review status:ACCEPTED

10 Apr 2020Submitted to PROTEINS: Structure, Function, and Bioinformatics
14 Apr 2020Submission Checks Completed
14 Apr 2020Assigned to Editor
21 May 2020Reviewer(s) Assigned
22 Jun 2020Review(s) Completed, Editorial Evaluation Pending
05 Jul 2020Editorial Decision: Revise Minor
22 Jul 20201st Revision Received
23 Jul 2020Submission Checks Completed
23 Jul 2020Assigned to Editor
23 Jul 2020Reviewer(s) Assigned
23 Jul 2020Review(s) Completed, Editorial Evaluation Pending
26 Jul 2020Editorial Decision: Accept