Tree-based Secondary Structure Interactions Predictor Method for Protein Contact Maps

Authors

  • Julio César Quintana-Zaez University of Ciego de Ávila "Máximo Gómez Báez", Ciego de Ávila, Cuba
  • Reynaldo Molina-Ruiz Central University "Marta Abreu" of the Villas, Santa Clara, Cuba
  • Cosme Ernesto Santiesteban-Toca University of Ciego de Ávila "Máximo Gómez Báez", Ciego de Ávila, Cuba

DOI:

https://doi.org/10.13053/cys-22-4-2827

Keywords:

Contact maps, folding patterns, decision trees, long-range contacts

Abstract

Understanding the folding of proteins is one of the most interesting research field for the Bioinformatics. The contact maps constitute an intermediate step in the prediction of the 3D structure of the proteins and allow to represent folding patterns. Currently, the methods used to predict contact maps achieve low precision results, only about 25% of long-range (L/5) contacts are correctly predicted, and their knowledge base is not humanly interpretable. In this paper, we propose an easy implementation multiple classifier for contact maps, which is based on patterns of interaction between secondary structures and employed decision trees as base classifiers. This method is able to naturally reduce the level of imbalance between contact/non-contact classes. In addition, a set of interpretable rules are extracted as a complement to the prediction. The validation of method performance shows that an average of 45% of general contacts are correctly predicted. Moreover, a Z-score comparison of its long-range contacts predictions (L/5) with participant methods in CASP11 competition shows that it is competitive with the state-of-the-art methods

Author Biography

Cosme Ernesto Santiesteban-Toca, University of Ciego de Ávila "Máximo Gómez Báez", Ciego de Ávila, Cuba

University of Ciego de Ávila “Máximo Gómez Báez”, Bioplantas Research Center

Downloads

Additional Files

Published

2018-12-30

Issue

Vol. 22 No. 4 (2018): Topic Trends in Computing Research (Guest Editors: A. Aguilar-Meléndez, E. Moya-Sánchez)

Section

Articles

License 

Hereby I transfer exclusively to the Journal "Computación y 
Sistemas", published by the Computing Research Center (CIC-IPN),
the Copyright of the aforementioned paper. I also accept that these 
rights will not be transferred to any other publication, in any other 
format, language or other existing means of developing.
I certify that the paper has not been previously disclosed or simultaneo
usly submitted to any other publication, and that it does not contain 
material whose publication would violate the Copyright or other 
proprietary rights of any person, company or institution. I certify that 
I have the permission from the institution or company where I work or 
study to publish this work.
The representative author accepts the responsibility for the publication
of this paper on behalf of each and every one of the authors. 
This transfer is subject to the following conditions:
  • The authors retain all ownership rights (such as patent rights) of this work, except for the publishing rights transferred to the CIC, through this document.
  • Authors retain the right to publish the work in whole or in part in any book they are the authors or publishers. They can also make use of this work in conferences, courses, personal web pages, and so on.
  • Authors may include working as part of his thesis, for non-profit distribution only.