Gydo C. P. van Zundert

Utrecht University — Netherlands

Biochemistry, Genetics and Molecular Biology · Life Sciences

20h-index4.4kcitations31works389.02yr avg
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Research Topics

Protein Structure and Dynamics(14), Enzyme Structure and Function(10), Advanced Electron Microscopy Techniques and Applications(9), Machine Learning in Materials Science(6), RNA and protein synthesis mechanisms(5)

Publications31 total

The HADDOCK2.4 web server for integrative modeling of biomolecular complexes
Nature Protocols·2024· 389 cited
Structural basis for recognition of N-formyl peptides as pathogen-associated molecular patterns
Nature Communications·2022· 53 citedOpen Access
Structural basis for isoform-specific inhibition of human CTPS1
Proceedings of the National Academy of Sciences·2021· 44 citedOpen Access
Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality
Structure·2021· 64 citedOpen Access
<scp>qFit</scp> 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle <scp>cryo‐EM</scp> density maps
Protein Science·2020· 74 citedOpen Access
qFit 3: Protein and ligand multiconformer modeling for X-ray crystallographic and single-particle cryo-EM density maps
2020· 10 citedOpen Access
Macromolecular refinement of X-ray and cryo-electron microscopy structures with Phenix / OPLS3e for improved structure and ligand quality
2020· 6 citedOpen Access
GemSpot: A Pipeline for Robust Modeling of Ligands into Cryo-EM Maps
Structure·2020· 72 citedOpen Access
GemSpot: A Pipeline for Robust Modeling of Ligands into CryoEM Maps
2019· 7 citedOpen Access
<i>qFit-ligand</i> Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps
Journal of Medicinal Chemistry·2018· 67 citedOpen Access
A multiconformer ligand model of inhibitor 53W bound to CREB binding protein bromodomain
2018· 41 cited
A multiconformer ligand model of EK6 bound to ERK2
2018
Qfit-Ligand Reveals Widespread Conformational Heterogeneity Of Drug-Like Molecules In X-Ray Electron Density Maps
Zenodo (CERN European Organization for Nuclear Research)·2018· 3 citedOpen Access
Qfit-Ligand Reveals Widespread Conformational Heterogeneity Of Drug-Like Molecules In X-Ray Electron Density Maps
2018Open Access
<i>qFit-ligand</i> reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps
2018· 3 citedOpen Access
HADDOCK
2018· 1 cited
Sense and Simplicity in HADDOCK Scoring: Lessons from CASP‐CAPRI (page 418)
Proteins Structure Function and Bioinformatics·2017· 35 citedOpen Access
The DisVis and PowerFit Web Servers: Explorative and Integrative Modeling of Biomolecular Complexes
Journal of Molecular Biology·2016· 61 citedOpen Access
Sense and simplicity in <scp>HADDOCK</scp> scoring: Lessons from <scp>CASP‐CAPRI</scp> round 1
Proteins Structure Function and Bioinformatics·2016· 62 citedOpen Access
Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF
Nature Communications·2016· 20 citedOpen Access
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Frequent Co-authors

Alexandre M. J. J. Bonvin(15), Kenneth Borrelli(11), Mikaël Trellet(8), Adrien S. J. Melquiond(8), D.A. Keedy(8), James S. Fraser(7), Henry van den Bedem(7), Ezgi Karaca(6), Brandi M. Hudson(6), Amélie Héliou(6), Tyler Day(6), João Rodrigues(5), Panagiotis L. Kastritis(5), Marc van Dijk(5), Rasmus Fonseca(5), Pooja Suresh(5), Zeynep Kurkcuoglu(5), Jörg Schaarschmidt(4), Saulo H. P. de Oliveira(4), Carl Schmitz(3)