A Similarity Search Algorithm to Predict Protein Structures (original) (raw)

Abstract

Accurate prediction of protein structures is very important for many applications such as drug discovery and biotechnology. Building side chains is an essential to get any reliable prediction of the protein structure for any given a protein main chain conformation. Most of the methods that predict side chain conformations use statistically generated data from known protein structures. It is a computationally intractable problem to search suitable side chains from all possible rotamers simultaneously using information of known protein structures. Reducing the number of possibility is a main issue to predict side chain conformation. This paper proposes an enumeration based similarity search algorithm to predict side chain conformations. By introducing “beam search” technique, a significant number of unrelated side chain rotamers can easily be eliminated. As a result, we can search for suitable residue side chains from all possible side chain conformations.

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Authors and Affiliations

  1. School of Information Technology, Deakin University, 3125, VIC, Australia
    Jiyuan An & Yi-Ping Phoebe Chen
  2. Australian Research Council Centre in Bioinformatics,
    Yi-Ping Phoebe Chen

Authors

  1. Jiyuan An
  2. Yi-Ping Phoebe Chen

Editor information

Editors and Affiliations

  1. School of Design, Engineering and Computing, Bournemouth University, UK
    Bogdan Gabrys
  2. Centre for SMART Systems, School of Environment and Technology, University of Brighton, BN2 4GJ, Brighton, UK
    Robert J. Howlett
  3. School of Electrical and Information Engineering, Knowledge Based Intelligent Engineering Systems Centre, University of South Australia, SA, 5095, Mawson Lakes, Australia
    Lakhmi C. Jain

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© 2006 Springer-Verlag Berlin Heidelberg

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An, J., Chen, YP.P. (2006). A Similarity Search Algorithm to Predict Protein Structures. In: Gabrys, B., Howlett, R.J., Jain, L.C. (eds) Knowledge-Based Intelligent Information and Engineering Systems. KES 2006. Lecture Notes in Computer Science(), vol 4252. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11893004\_165

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