Comparison with other tools

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    SPILLOproject team

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Comparison with other tools

by SPILLOproject team

  • visibility Read 268 times


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    Comparison with traditional structure-based approaches

    SPILLO-PBSS has been compared with other available tools which could be used for the prediction of binding sites within protein 3D-structures, each tool being representative of a different class of methods.

    Tests were performed on limit cases concerning the conformation of the binding site. In particular, a search for the binding site of the ligand 'Guanosine diphosphate (GDP)' was performed within four H-Ras protein conformations, in which various levels of distortion of the binding site are taken into account: (i) SUITABLY OPEN (undistorted); (ii) WIDE-OPEN; (iii) WIDE-OPEN and OCCUPIED; (iv) COMPLETELY CLOSED.

    Results are reported in Table 2.

       

    SPILLO-PBSS has proved successful in recognizing binding sites even within really distorted proteins. No method (apart from SPILLO-PBSS) has ever been able to recognize the expected binding site when COMPLETELY CLOSED and apparently INACCESSIBLE to the ligand.

    > The following VIDEO shows the most difficult situation where the GDP binding site is COMPLETELY CLOSED. All regions of the protein are analysed, included those right inside the protein, which cannot be reached by traditional structure-based approaches. 

                                                   

      

      > On the left (for reference): RAS protein in its GDP complexed form (PDB code: 4q21), with suitably open GDP binding site.

      > On the right:  Successfull identification of the completely closed GDP binding site by SPILLO-PBSS

     



    *) FOR FULL DETAILS SEE THE REFERENCE PAPER:

    SPILLO-PBSS: Detecting hidden binding sites within protein 3D-structures through a flexible structure-based approach,  A. Di Domizio et al, Journal of Computational Chemistry, 2014, 35 (27): 2005-2017. DOI: 10.1002/jcc.23714