Webinar by Prof. Alexandre M.J.J. Bonvin
Computational Structural Biology Group, Utrecht University (The Netherlands)
Integrative modelling of biomolecular complexes with HADDOCK
The prediction of the quaternary structure of biomolecular macromolecules is of paramount importance for fundamental understanding of cellular processes and drug design. In the era of integrative structural biology, one way of increasing the accuracy of modelling methods used to predict the structure of biomolecular complexes is to include as much experimental or predictive information as possible in the process.
We have developed for this purpose a versatile information-driven docking approach HADDOCK (http://www.bonvinlab.org/software/haddock2.2) [1-3]. HADDOCK can integrate information derived from biochemical, biophysical or bioinformatics methods to enhance sampling, scoring, or both [4]. The information that can be integrated is quite diverse: interface restraints from NMR, mutagenesis experiments, or bioinformatics predictions; shape data from small-angle X-ray scattering [5] and, recently, cryo-electron microscopy experiments [6].
References
G.C.P van Zundert, J.P.G.L.M. Rodrigues, M. Trellet, C. Schmitz, P.L. Kastritis, E. Karaca, A.S.J. Melquiond, M. van Dijk, S.J. de Vries and A.M.J.J. Bonvin. The HADDOCK2.2 webserver: User-friendly integrative modeling of biomolecular complexes. J. Mol. Biol., 428, 720-725 (2015).
S.J. de Vries, M. van Dijk and A.M.J.J. Bonvin The HADDOCK web server for data-driven biomolecular docking. Nature Protocols, 5, 883-897 (2010).
C. Dominguez, R. Boelens and A.M.J.J. Bonvin HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737 (2003).
J.P.G.L.M Rodrigues and A.M.J.J. Bonvin Integrative computational modeling of protein interactions. FEBS J., 281, 1988-2003 (2014).
E. Karaca and A.M.J.J. Bonvin. On the usefulness of Ion Mobility Mass Spectrometry and SAXS data in scoring docking decoys. Acta Cryst. D., D69, 683-694 (2013).
G.C.P. van Zundert, A.S.J. Melquiond and A.M.J.J. Bonvin. Integrative modeling of biomolecular complexes: HADDOCKing with Cryo-EM data. Structure. 23, 949-960 (2015).”