Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies

M. A. Messih, R. Lepore, Paolo Marcatili, A. Tramontano

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    Abstract

    Motivation: Antibodies are able to recognize a wide range of antigens through their complementary determining regions formed by six hypervariable loops. Predicting the 3D structure of these loops is essential for the analysis and reengineering of novel antibodies with enhanced affinity and specificity. The canonical structure model allows high accuracy prediction for five of the loops. The third loop of the heavy chain, H3, is the hardest to predict because of its diversity in structure, length and sequence composition. Results: We describe a method, based on the Random Forest automatic learning technique, to select structural templates for H3 loops among a dataset of candidates. These can be used to predict the structure of the loop with a higher accuracy than that achieved by any of the presently available methods. The method also has the
    advantage of being extremely fast and returning a reliable estimate of the model quality.
    Original languageEnglish
    JournalBioinformatics
    Volume30
    Issue number19
    Pages (from-to)2733-2740
    ISSN1367-4803
    DOIs
    Publication statusPublished - 2014

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