An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45.

Koukos, P. I.; Roel-Touris, J.; Ambrosetti, F.; Geng, C.; Schaarschmidt, J.; Trellet, M. E.; Melquiond, A. S. J.; Xue, L.; Vargas Honorato, R.; Moreira, I.; Kurkcuoglu, Z.; Vangone, A.; Bonvin, A. M. J. J.

doi:10.1101/718122

bioRxiv · 10.1101/718122

An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45.

Koukos, P. I.·Roel-Touris, J.·Ambrosetti, F.·Geng, C.·Schaarschmidt, J.·Trellet, M. E.·Melquiond, A. S. J.·Xue, L.·Vargas Honorato, R.·Moreira, I.·Kurkcuoglu, Z.·Vangone, A.·Bonvin, A. M. J. J.

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Abstract

Our information-driven docking approach HADDOCK has demonstrated a sustained performance since the start of its participation to CAPRI. This is due, in part, to its ability to integrate data into the modelling process, and to the robustness of its scoring function. We participated in CAPRI both as server and as manual predictors.\n\nIn CAPRI rounds 38-45, we have used various strategies depending on the information at hand. These ranged from imposing restraints to a few residues identified from literature as being important for the interaction, to binding pockets identified from homologous complexes or template-based refinement / CA-CA restraint-guided docking from identified templates. When relevant, symmetry restraints were used to limit the conformational sampling. We also tested for a large decamer target a new implementation of the MARTINI coarse-grained force field in HADDOCK. Overall in the current rounds, we obtained acceptable or better predictions for 13 and 11 server and manual submissions, respectively, out of the 22 interfaces. Our server performance (acceptable models) was better (59%) than the manual (50%) one, in which we typically experiment with various combinations of protocols and data sources. Again, our simple scoring function based on a linear combination of intermolecular van der Waals and electrostatic energies and an empirical desolvation term demonstrated a good performance in the scoring experiment with a 63% success rate across all 22 interfaces.\n\nAn analysis of model quality indicates that, while we are consistently performing well in generating acceptable models, there is room for improvement for generating/identifying higher quality models.

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Koukos, P. I., Roel-Touris, J., Ambrosetti, F., Geng, C., Schaarschmidt, J., Trellet, M. E., Melquiond, A. S. J., Xue, L., Vargas Honorato, R., Moreira, I., Kurkcuoglu, Z., Vangone, A., Bonvin, A. M. J. J.. 2019-07-29. An overview of data-driven HADDOCK strategies in CAPRI rounds 38-45.. https://doi.org/10.1101/718122

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