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Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain–domain assembly and protein-RNA binding by Carles Pons; Albert Solernou; Laura Perez-Cano; Solène Grosdidier; Juan Fernandez-Recio is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain–domain assembly and protein-RNA binding about?
## 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, o
Who reads Optimization of pyDock for the new CAPRI challenges: Docking of homology-based models, domain–domain assembly and protein-RNA binding?
It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- Carles Pons; Albert Solernou; Laura Perez-Cano; Solène Grosdidier; Juan Fernandez-Recio
- Publisher
- John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)
- Published
- 2010
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)