A novel model-based on FCM-LM algorithm for prediction of protein folding rate

Journal of Bioinformatics and Computational Biology
Longlong LiuJing Cui

Abstract

The prediction of protein folding rates is of paramount importance in describing the protein folding mechanism, which has broad applications in fields such as enzyme engineering and protein engineering. Therefore, predicting protein folding rates using the first-order of protein sequence, secondary structure and amino acid properties has become a very active research topic in recent years. This paper presents a new fuzzy cognitive map (FCM) model based on deep learning neural networks which uses data obtained from biological experiments to predict the protein folding rate. FCM extracts the important data features from the protein sequence which then initializes the deep neural networks effectively. It was found that the Levenberg-Marquardt (LM) algorithm for deep neural networks can improve the prediction accuracy of the protein folding rates. The correlation coefficient between the predicted values and those real values obtained from experiments reached 0.94 and 0.9 in two independent numerical tests.

References

Nov 23, 2000·Journal of Biomolecular Structure & Dynamics·M M GromihaA Sarai
Jun 13, 2006·Neural Computation·Geoffrey E HintonYee-Whye Teh
Mar 21, 2008·Journal of Computational Chemistry·Liang-Tsung Huang, M Michael Gromiha
Aug 30, 2008·Journal of Computational Chemistry·Yingfu JiangLukasz Kurgan
Oct 10, 2008·Nucleic Acids Research·Natalya S BogatyrevaDmitry N Ivankov
Jul 10, 2010·Bioinformatics·Liang-Tsung Huang, M Michael Gromiha
Dec 14, 2011·Amino Acids·Jitao T HuangWei Huang
Nov 28, 2012·Science·Ken A Dill, Justin L MacCallum
Feb 15, 2014·World Journal of Clinical Cases·Carlton Robert FenzlJason Goldsmith
Jun 11, 2016·Methods : a Companion to Methods in Enzymology·Tianchuan DuBilin Sun

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Citations

Oct 16, 2019·Protein and Peptide Letters·Yanru LiJun Lv

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