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An overview of data‐driven HADDOCK strategies in CAPRI rounds 38‐45
Author(s) -
Koukos Panagiotis I.,
RoelTouris Jorge,
Ambrosetti Francesco,
Geng Cunliang,
Schaarschmidt Jörg,
Trellet Mikael E.,
Melquiond Adrien S. J.,
Xue Li C.,
Honorato Rodrigo V.,
Moreira Irina,
Kurkcuoglu Zeynep,
Vangone Anna,
Bonvin Alexandre M. J. J.
Publication year - 2020
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.25869
Subject(s) - computer science , van der waals force , robustness (evolution) , haddock , docking (animal) , template , data mining , chemistry , biology , medicine , biochemistry , nursing , organic chemistry , molecule , gene , programming language , fishery , fish <actinopterygii>
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 modeling process, and to the robustness of its scoring function. We participated in CAPRI both as server and manual predictors. In CAPRI rounds 38‐45, we have used various strategies depending on the available information. 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, we obtained acceptable or better predictions for 13 and 11 server and manual submissions, respectively, out of the 22 interfaces. Our server performance (acceptable or higher‐quality models when considering the top 10) 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. An 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.