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

Koukos, Panagiotis I.; Roel-Touris, Jorge; Ambrosetti, Francesco; Geng, Cunliang; Schaarschmidt, Jörg ORCID iD icon 1; Trellet, Mikael E.; Melquiond, Adrien S. J.; Xue, Li C.; Honorato, Rodrigo V.; Moreira, Irina; Kurkcuoglu, Zeynep; Vangone, Anna; Bonvin, Alexandre M. J. J.
1 Institut für Nanotechnologie (INT), Karlsruher Institut für Technologie (KIT)


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. ... mehr

Verlagsausgabe §
DOI: 10.5445/IR/1000105992
Veröffentlicht am 21.02.2020
DOI: 10.1002/prot.25869
Zitationen: 8
Web of Science
Zitationen: 8
Zitationen: 11
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Nanotechnologie (INT)
Publikationstyp Zeitschriftenaufsatz
Publikationsmonat/-jahr 08.2020
Sprache Englisch
Identifikator ISSN: 0887-3585, 1097-0134
KITopen-ID: 1000105992
HGF-Programm 43.21.04 (POF III, LK 01) Molecular Engineering
Erschienen in Proteins
Verlag Wiley-Liss
Band 88
Heft 8
Seiten 1029-1036
Vorab online veröffentlicht am 30.12.2019
Schlagwörter biomolecular interactions, complexes, integrative modeling, prediction, scoring
Nachgewiesen in Dimensions
Web of Science
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