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  • Comparing atom-based with residue based descriptors in predicting binding site similarity: do backbone atoms matter?

    Author(s)
    Sturm, Noe
    Rognan, Didier
    Quinn, Ronald J
    Kellenberger, Esther
    Griffith University Author(s)
    Quinn, Ronald J.
    Year published
    2016
    Metadata
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    Abstract
    Aim: We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction. Results: We modified the in-house program SiteAlign to replace generic pharmacophoric descriptors of cavity-lining amino acids by descriptors accounting for solvent exposure. Benchmarking the novel, atom-based, method (SiteAlign2) revealed no global improvement of performance. However, in the rare cases of no sequence or global structure similarities between the compared proteins, SiteAlign2 was more successful if backbone atoms are key determinants of ligand binding. Conclusion: ...
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    Aim: We question the level of detail required in protein 3D-representation to detect site similarity which is relevant for polypharmacology prediction. Results: We modified the in-house program SiteAlign to replace generic pharmacophoric descriptors of cavity-lining amino acids by descriptors accounting for solvent exposure. Benchmarking the novel, atom-based, method (SiteAlign2) revealed no global improvement of performance. However, in the rare cases of no sequence or global structure similarities between the compared proteins, SiteAlign2 was more successful if backbone atoms are key determinants of ligand binding. Conclusion: SiteAlign suits the comparison of binding sites for close or distant homologs. SiteAlign2 provides a better insight into the physical model of site similarity between nonhomologs, but at the expense of an increased sensitivity to atomic coordinates.
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    Journal Title
    Future Medicinal Chemistry
    Volume
    8
    Issue
    15
    DOI
    https://doi.org/10.4155/fmc-2016-0077
    Subject
    Medicinal and biomolecular chemistry
    Medicinal and biomolecular chemistry not elsewhere classified
    Pharmacology and pharmaceutical sciences
    Publication URI
    http://hdl.handle.net/10072/100568
    Collection
    • Journal articles

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