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    Multi-Regional Analysis of Contact Maps for Protein Structure Prediction

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    Ahmed_Hazem_R_200904_MSC.pdf (2.660Mb)
    Date
    2009-04-24
    Author
    Ahmed, Hazem Radwan A.
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    Abstract
    1D protein sequences, 2D contact maps and 3D structures are three different

    representational levels of detail for proteins. Predicting protein 3D

    structures from their 1D sequences remains one of the complex challenges of

    bioinformatics. The "Divide and Conquer" principle is applied in our

    research to handle this challenge, by dividing it into two separate yet

    dependent subproblems, using a Case-Based Reasoning (CBR) approach. Firstly,

    2D contact maps are predicted from their 1D protein sequences; secondly, 3D

    protein structures are then predicted from their predicted 2D contact maps.

    We focus on the problem of identifying common substructural patterns of

    protein contact maps, which could potentially be used as building blocks for

    a bottom-up approach for protein structure prediction. We further

    demonstrate how to improve identifying these patterns by combining both

    protein sequence and structural information. We assess the consistency and

    the efficiency of identifying common substructural patterns by conducting

    statistical analyses on several subsets of the experimental results with

    different sequence and structural information.
    URI for this record
    http://hdl.handle.net/1974/1789
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