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Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain–domain assembly and protein-RNA binding

Authors

  • Carles Pons,

    1. Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
    2. Computational Bioinformatics, National Institute of Bioinformatics (INB), Barcelona, Spain
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    • The authors state no conflict of interest.

  • Albert Solernou,

    1. Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
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    • The authors state no conflict of interest.

  • Laura Perez-Cano,

    1. Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
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  • Solène Grosdidier,

    1. Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
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  • Juan Fernandez-Recio

    Corresponding author
    1. Life Sciences, Barcelona Supercomputing Center, Barcelona, Spain
    • Barcelona Supercomputing Center (BSC), Jordi Girona 29, 08034 Barcelona, Spain
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    • The authors state no conflict of interest.


Abstract

We describe here our results in the last CAPRI edition. We have participated in all targets, both as predictors and as scorers, using our pyDock docking methodology. The new challenges (homology-based modeling of the interacting subunits, domain–domain assembling, and protein-RNA interactions) have pushed our computer tools to the limits and have encouraged us to devise new docking approaches. Overall, the results have been quite successful, in line with previous editions, especially considering the high difficulty of some of the targets. Our docking approaches succeeded in five targets as predictors or as scorers (T29, T34, T35, T41, and T42). Moreover, with the inclusion of available information on the residues expected to be involved in the interaction, our protocol would have also succeeded in two additional cases (T32 and T40). In the remaining targets (except T37), results were equally poor for most of the groups. We submitted the best model (in ligand RMSD) among scorers for the unbound-bound target T29, the second best model among scorers for the protein-RNA target T34, and the only correct model among predictors for the domain assembly target T35. In summary, our excellent results for the new proposed challenges in this CAPRI edition showed the limitations and applicability of our approaches and encouraged us to continue developing methodologies for automated biomolecular docking. Proteins 2010. © 2010 Wiley-Liss, Inc.

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