A Bi-LSTM Based Ensemble Algorithm for Prediction of Protein Secondary Structure

[1]  L. Kier,et al.  Amino acid side chain parameters for correlation studies in biology and pharmacology. , 2009, International journal of peptide and protein research.

[2]  Kuldip K. Paliwal,et al.  Capturing non‐local interactions by long short‐term memory bidirectional recurrent neural networks for improving prediction of protein secondary structure, backbone angles, contact numbers and solvent accessibility , 2017, Bioinform..

[3]  Kenji Mizuguchi,et al.  Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites , 2010, Bioinform..

[4]  James G. Lyons,et al.  Improving prediction of secondary structure, local backbone angles, and solvent accessible surface area of proteins by iterative deep learning , 2015, Scientific Reports.

[5]  Yaoqi Zhou,et al.  Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks , 2018, Bioinform..

[6]  B. Rost.  Review: protein secondary structure prediction continues to rise. , 2001, Journal of structural biology.

[7]  Yaohang Li,et al.  Context-Based Features Enhance Protein Secondary Structure Prediction Accuracy , 2014, J. Chem. Inf. Model..

[8]  B. Matthews.  Comparison of the predicted and observed secondary structure of T4 phage lysozyme. , 1975, Biochimica et biophysica acta.

[9]  Yaoqi Zhou,et al.  Improving protein disorder prediction by deep bidirectional long short‐term memory recurrent neural networks , 2016, Bioinform..

[10]  Tara N. Sainath,et al.  FUNDAMENTAL TECHNOLOGIES IN MODERN SPEECH RECOGNITION Digital Object Identifier 10.1109/MSP.2012.2205597 , 2012 .

[11]  C Geourjon,et al.  SOPM: a self-optimized method for protein secondary structure prediction. , 1994, Protein engineering.

[12]  Jian Peng,et al.  Protein Secondary Structure Prediction Using Deep Convolutional Neural Fields , 2015, Scientific Reports.

[13]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[14]  Arne Elofsson,et al.  SubCons: a new ensemble method for improved human subcellular localization predictions , 2017, Bioinform..

[15]  Nitish Srivastava,et al.  Dropout: a simple way to prevent neural networks from overfitting , 2014, J. Mach. Learn. Res..

[16]  B. Rost,et al.  Prediction of protein secondary structure at better than 70% accuracy. , 1993, Journal of molecular biology.

[17]  Jürgen Schmidhuber,et al.  Long Short-Term Memory , 1997, Neural Computation.

[18]  A. Biegert,et al.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.

[19]  Kevin Karplus,et al.  SAM-T08, HMM-based protein structure prediction , 2009, Nucleic Acids Res..

[20]  J. Onuchic,et al.  Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. , 2003, Journal of molecular biology.

[21]  Hailong Hu,et al.  Protein secondary structure prediction based on the fuzzy support vector machine with the hyperplane optimization. , 2018, Gene.

[22]  Jing Wang,et al.  A new hybrid coding for protein secondary structure prediction based on primary structure similarity. , 2017, Gene.

[23]  Bernard F. Buxton,et al.  Secondary structure prediction with support vector machines , 2003, Bioinform..

[24]  B. Rost,et al.  A modified definition of Sov, a segment‐based measure for protein secondary structure prediction assessment , 1999, Proteins.

[25]  Wei Li,et al.  RaptorX-Property: a web server for protein structure property prediction , 2016, Nucleic Acids Res..

[26]  Dong Xu,et al.  MUPRED: A tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction , 2006, Proteins.

[27]  Christian Cole,et al.  JPred4: a protein secondary structure prediction server , 2015, Nucleic Acids Res..