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Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction

Journal of Molecular Modeling volume 18, pages 4275–4289 (2012)Cite this article

Abstract

Computational methods are rapidly gaining importance in the field of structural biology, mostly due to the explosive progress in genome sequencing projects and the large disparity between the number of sequences and the number of structures. There has been an exponential growth in the number of available protein sequences and a slower growth in the number of structures. There is therefore an urgent need to develop computational methods to predict structures and identify their functions from the sequence. Developing methods that will satisfy these needs both efficiently and accurately is of paramount importance for advances in many biomedical fields, including drug development and discovery of biomarkers. A novel method called fast learning optimized prediction methodology (FLOPRED) is proposed for predicting protein secondary structure, using knowledge-based potentials combined with structure information from the CATH database. A neural network-based extreme learning machine (ELM) and advanced particle swarm optimization (PSO) are used with this data that yield better and faster convergence to produce more accurate results. Protein secondary structures are predicted reliably, more efficiently and more accurately using FLOPRED. These techniques yield superior classification of secondary structure elements, with a training accuracy ranging between 83 % and 87 % over a widerange of hidden neurons and a cross-validated testing accuracy ranging between 81 % and 84 % and a segment overlap (SOV) score of 78 % that are obtained with different sets of proteins. These results are comparable to other recently published studies, but are obtained with greater efficiencies, in terms of time and cost.

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Acknowledgements

The algorithm for knowledge-based potentials data, was developed by members from the Kolinski [32] lab. We would like to thank Dr. John Orban for providing us with the sequences for the switching proteins. This work was supported by the National Institutes of Health grants R01GM081680, R01GM072014 and National Science Foundation grant IGERT-0504304.

Author information

Affiliations

  1. Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, 700 Children’s Drive, Columbus, OH, USA

    S. Saraswathi

  2. Department of Mathematics, University of Oviedo, Oviedo, Spain

    J. L. Fernández-Martínez

  3. Laboratory of Theory of Biopolymers, Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland

    A. Kolinski

  4. Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA

    R. L. Jernigan

  5. Battelle Center for Mathematical Medicine, The Research Institute at Nationwide Children’s Hospital, Department of Pediatrics, The Ohio State University College of Medicine, 700 Children’s Drive, Columbus, OH, 43205, USA

    A. Kloczkowski

Authors
  1. S. Saraswathi
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  2. J. L. Fernández-Martínez
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  3. A. Kolinski
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  4. R. L. Jernigan
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  5. A. Kloczkowski
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Corresponding author

Correspondence to A. Kloczkowski.

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Saraswathi, S., Fernández-Martínez, J.L., Kolinski, A. et al. Fast learning optimized prediction methodology (FLOPRED) for protein secondary structure prediction. J Mol Model 18, 4275–4289 (2012). https://doi.org/10.1007/s00894-012-1410-7

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  • DOI: https://doi.org/10.1007/s00894-012-1410-7

Keywords

  • Knowledge-based potentials
  • Machine learning
  • Neural networks
  • Particle swarm optimization
  • Protein secondary structure prediction