User-Friendly Integrative Modeling of Biomolecular Complexes

Autor: van Zundert, G.C.P., Bonvin, A.M.J.J., Rodrigues, J.P.G.L.M., Trellet, M., Schmitz, C., Kastritis, P.L., Karaca, E., Melquiond, A.S.J., van Dijk, M., de Vries, S.J.

Publikováno v: NARCIS
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Datacite
Journal of Molecular Biology, 428(4), 720. Academic Press Inc.
Journal of Molecular Biology, 428(4), 720-5. Academic Press Inc.
Journal of Molecular Biology, 428(4), 720
Journal of Molecular Biology 428(4) 720–725

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

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=dedup_wf_001::84cc6d5f27cfdfa932b18082e8faaefd
https://www.mendeley.com/catalogue/haddock22-web-server-userfriendly-integrative-modeling-biomolecular-complexes/

Data-driven docking: HADDOCK's adventures in CAPRI

Autor: van Dijk, A.D.J., de Vries, S.J., Dominguez, C., Chen, H., Zhou, H.-X., Bonvin, A.M.J.J., NMR-spectroscopie, NMR Spectroscopy 1, Dep Scheikunde

Publikováno v: Proteins: Structure function and bioinformatics, 60, 232. Wiley-Liss Inc.

We have shown previously that given high-resolution structures of the unbound molecules, structure determination of protein com- plexes is possible by including biochemical and/or biophysical data as highly ambiguous distance re- straints in a dockin

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::603da72bfbf37b20cba4c908ed0a0647
https://doi.org/10.1002/prot.20563

Haddock

Autor: Bonvin, A.M.J.J., van Dijk, M., Karaca, E., Kastritis, P., Melquiond, A.S.J., Schmitz, C., de Vries, S.J., Roberts, G.C.K.

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=od_______101::bc8726c741b9ec754a0e4e222c06d348
https://dspace.library.uu.nl/handle/1874/385179

Protein–Protein Docking with HADDOCK

Autor: Schmitz, C., Melquiond, A.S.J., de Vries, S.J., Karaca, E., van Dijk, M., Kastritis, P., Bonvin, A.M.J.J., Bertini, Ivano, McGreevy, Kathleen S., Parigi, Giacomo, NMR Spectroscopy, Sub NMR Spectroscopy

Publikováno v: NMR of Biomolecules
NMR of biomolecules : towards mechanistic systems biology, 520. Wiley
STARTPAGE=520;TITLE=NMR of biomolecules : towards mechanistic systems biology

Advances in biophysics and biochemistry have pushed back the limits of the structural characterization of biomolecular assemblies. Mixing even a limited amount of experimental and/or bioinformatics data with modeling methods such as macromolecular do

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::a99ad6e438a5dc243f25bcb67818a5e5
https://doi.org/10.1002/9783527644506.ch32

SQUEEZE-E: The optimal solution for molecular simulations with periodic boundary conditions

Autor: Wassenaar, T.A., de Vries, S.J., Bonvin, A.M.J.J., Bekker, H., NMR Spectroscopy, Sub NMR Spectroscopy

Publikováno v: Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation, 8(10), 3618. American Chemical Society
Journal of Chemical Theory and Computation, 8(10), 3618-3627
Journal of Chemical Theory and Computation, 8(10), 3618
ICT FP7 Publications Database
NARCIS
Journal of Chemical Theory and Computation, 8(10), 3618-3627. AMER CHEMICAL SOC

In molecular simulations of macromolecules, it is desirable to limit the amount of solvent in the system to avoid spending computational resources on uninteresting solvent−solvent interactions. As a consequence, periodic boundary conditions are com

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c7a5b8857800032937254c93ea323dd3
https://dspace.library.uu.nl/handle/1874/256773