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Artificial Neural Networks

Volume 1260 of the series Methods in Molecular Biology pp 165-178

Date:

GENN: A GEneral Neural Network for Learning Tabulated Data with Examples from Protein Structure Prediction

  • Eshel FaraggiAffiliated withDepartment of Biochemistry and Molecular Biology, Indiana University School of Medicine, IndianapolisBattelle Center for Mathematical Medicine, Nationwide Children’s HospitalPhysics Division, Research and Information Systems, LLC Email author 
  • , Andrzej KloczkowskiAffiliated withBattelle Center for Mathematical Medicine, Nationwide Children’s HospitalDepartment of Pediatrics, The Ohio State University Email author 

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Abstract

We present a GEneral Neural Network (GENN) for learning trends from existing data and making predictions of unknown information. The main novelty of GENN is in its generality, simplicity of use, and its specific handling of windowed input/output. Its main strength is its efficient handling of the input data, enabling learning from large datasets. GENN is built on a two-layered neural network and has the option to use separate inputs–output pairs or window-based data using data structures to efficiently represent input–output pairs. The program was tested on predicting the accessible surface area of globular proteins, scoring proteins according to similarity to native, predicting protein disorder, and has performed remarkably well. In this paper we describe the program and its use. Specifically, we give as an example the construction of a similarity to native protein scoring function that was constructed using GENN. The source code and Linux executables for GENN are available from Research and Information Systems at http://​mamiris.​com and from the Battelle Center for Mathematical Medicine at http://​mathmed.​org. Bugs and problems with the GENN program should be reported to EF.

Key words

Neural network Protein scoring Windowed input Automatic learning GENN Protein structure prediction