research-article

A genetic algorithm to enhance transmembrane helices prediction

Authors:

Sanja Lazarova-MolnarAuthors Info & Claims

GECCO '11: Proceedings of the 13th annual conference on Genetic and evolutionary computation

Pages 347 - 354

https://doi.org/10.1145/2001576.2001624

Published: 12 July 2011 Publication History

Abstract

A transmembrane helix (TMH) topology prediction is becoming a central problem in bioinformatics because the structure of TM proteins is difficult to determine by experimental means. Therefore, methods which could predict the TMHs topologies computationally are highly desired. In this paper we introduce TMHindex, a method for detecting TMH segments solely by the amino acid sequence information. Each amino acid in a protein sequence is represented by a Compositional Index deduced from a combination of the difference in amino acid appearances in TMH and non-TMH segments in training protein sequences and the amino acid composition information. Furthermore, genetic algorithm was employed to find the optimal threshold value to separate TMH segments from non-TMH segments. The method successfully predicted 376 out of the 378 TMH segments in 70 testing protein sequences. The level of accuracy achieved using TMHindex in comparison to recent methods for predicting the topology of TM proteins is a strong argument in favor of our method.

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Cited By

Navaz AMohammed ESerhani MZaki N(2016)The use of data mining techniques to predict mortality and length of stay in an ICU2016 12th International Conference on Innovations in Information Technology (IIT)10.1109/INNOVATIONS.2016.7880045(1-5)Online publication date: Nov-2016
https://doi.org/10.1109/INNOVATIONS.2016.7880045
Shatnawi M(2016)Novel Tree-Based Proximity Search with SMOTE and Compositional Indexing Techniques for Protein Domain Identification2016 27th International Workshop on Database and Expert Systems Applications (DEXA)10.1109/DEXA.2016.029(71-75)Online publication date: Sep-2016
https://doi.org/10.1109/DEXA.2016.029
Shatnawi MYoo PMuhaidat S(2015)Protein Inter‐Domain Linker PredictionPattern Recognition in Computational Molecular Biology10.1002/9781119078845.ch12(212-235)Online publication date: 18-Dec-2015
https://doi.org/10.1002/9781119078845.ch12
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Index Terms

A genetic algorithm to enhance transmembrane helices prediction
1. Computing methodologies
  1. Artificial intelligence
    1. Search methodologies
      1. Heuristic function construction

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cover image ACM Conferences

GECCO '11: Proceedings of the 13th annual conference on Genetic and evolutionary computation

July 2011

2140 pages

ISBN:9781450305570

DOI:10.1145/2001576

Editor:
Natalio Krasnogor
University of Nottingham, UK
,
General Chair:
Pier Luca Lanzi
Politecnico di Milano, Italy

Copyright © 2011 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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SIGEVO: ACM Special Interest Group on Genetic and Evolutionary Computation

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Association for Computing Machinery

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Published: 12 July 2011

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GECCO '11

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SIGEVO

GECCO '11: Genetic and Evolutionary Computation Conference

July 12 - 16, 2011

Dublin, Ireland

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Overall Acceptance Rate 1,669 of 4,410 submissions, 38%

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Cited By

Navaz AMohammed ESerhani MZaki N(2016)The use of data mining techniques to predict mortality and length of stay in an ICU2016 12th International Conference on Innovations in Information Technology (IIT)10.1109/INNOVATIONS.2016.7880045(1-5)Online publication date: Nov-2016
https://doi.org/10.1109/INNOVATIONS.2016.7880045
Shatnawi M(2016)Novel Tree-Based Proximity Search with SMOTE and Compositional Indexing Techniques for Protein Domain Identification2016 27th International Workshop on Database and Expert Systems Applications (DEXA)10.1109/DEXA.2016.029(71-75)Online publication date: Sep-2016
https://doi.org/10.1109/DEXA.2016.029
Shatnawi MYoo PMuhaidat S(2015)Protein Inter‐Domain Linker PredictionPattern Recognition in Computational Molecular Biology10.1002/9781119078845.ch12(212-235)Online publication date: 18-Dec-2015
https://doi.org/10.1002/9781119078845.ch12
Shatnawi MZaki NAlba E(2013)Prediction of protein inter-domain linkers using compositional index and simulated annealingProceedings of the 15th annual conference companion on Genetic and evolutionary computation10.1145/2464576.2482740(1603-1608)Online publication date: 6-Jul-2013
https://dl.acm.org/doi/10.1145/2464576.2482740
Hayat MKhan A(2013)WRF-TMH: predicting transmembrane helix by fusing composition index and physicochemical properties of amino acidsAmino Acids10.1007/s00726-013-1466-444:5(1317-1328)Online publication date: 14-Mar-2013
https://doi.org/10.1007/s00726-013-1466-4

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