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Gydo Van Zundert
Gydo Van Zundert
Verified email at schrodinger.com - Homepage
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Year
The HADDOCK2. 2 web server: user-friendly integrative modeling of biomolecular complexes
GCP Van Zundert, J Rodrigues, M Trellet, C Schmitz, PL Kastritis, ...
Journal of molecular biology 428 (4), 720-725, 2016
24562016
Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment
MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ...
Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016
1682016
Probing a cell-embedded megadalton protein complex by DNP-supported solid-state NMR
M Kaplan, A Cukkemane, GCP Van Zundert, S Narasimhan, M DaniŽls, ...
Nature methods 12 (7), 649-652, 2015
1552015
Integrative modeling of biomolecular complexes: HADDOCKing with cryo-electron microscopy data
GCP van Zundert, ASJ Melquiond, AMJJ Bonvin
Structure 23 (5), 949-960, 2015
782015
Defining the limits of homology modeling in information‐driven protein docking
J Rodrigues, ASJ Melquiond, E Karaca, M Trellet, M Van Dijk, ...
Proteins: Structure, Function, and Bioinformatics 81 (12), 2119-2128, 2013
762013
Synthetic group A streptogramin antibiotics that overcome Vat resistance
Q Li, J Pellegrino, DJ Lee, AA Tran, HA Chaires, R Wang, JE Park, K Ji, ...
Nature 586 (7827), 145-150, 2020
742020
DisVis: quantifying and visualizing accessible interaction space of distance-restrained biomolecular complexes
GCP Van Zundert, AMJJ Bonvin
Bioinformatics 31 (19), 3222-3224, 2015
722015
Modeling protein–protein complexes using the HADDOCK webserver “modeling protein complexes with HADDOCK”
GCP van Zundert, AMJJ Bonvin
Protein structure prediction, 163-179, 2014
692014
GemSpot: a pipeline for robust modeling of ligands into cryo-EM maps
MJ Robertson, GCP van Zundert, K Borrelli, G Skiniotis
Structure 28 (6), 707-716. e3, 2020
562020
Sense and simplicity in HADDOCK scoring: Lessons from CASP‐CAPRI round 1
A Vangone, J Rodrigues, LC Xue, GCP Van Zundert, C Geng, ...
Proteins: Structure, Function, and Bioinformatics 85 (3), 417-423, 2017
552017
The DisVis and PowerFit web servers: explorative and integrative modeling of biomolecular complexes
GCP Van Zundert, M Trellet, J Schaarschmidt, Z Kurkcuoglu, M David, ...
Journal of molecular biology 429 (3), 399-407, 2017
532017
IR Spectroscopy of Isolated Neutral and Protonated Adenine and 9‐Methyladenine
GCP Van Zundert, S Jaeqx, G Berden, JM Bakker, K Kleinermanns, ...
ChemPhysChem 12 (10), 1921-1927, 2011
512011
qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps
GCP van Zundert, BM Hudson, SHP de Oliveira, DA Keedy, R Fonseca, ...
Journal of Medicinal Chemistry 61 (24), 11183-11198, 2018
502018
Fast and sensitive rigid-body fitting into cryo-EM density maps with PowerFit
G Cp van Zundert, A Mjj Bonvin
AIMS Biophysics 2 (2), 73-87, 2015
502015
qFit 3: Protein and ligand multiconformer modeling for X‐ray crystallographic and single‐particle cryo‐EM density maps
BT Riley, SA Wankowicz, SHP de Oliveira, GCP van Zundert, DW Hogan, ...
Protein Science 30 (1), 270-285, 2021
382021
Macromolecular refinement of X-ray and cryoelectron microscopy structures with Phenix/OPLS3e for improved structure and ligand quality
GCP van Zundert, NW Moriarty, OV Sobolev, PD Adams, KW Borrelli
Structure 29 (8), 913-921. e4, 2021
372021
Structural basis for isoform-specific inhibition of human CTPS1
EM Lynch, MA DiMattia, S Albanese, GCP van Zundert, JM Hansen, ...
Proceedings of the National Academy of Sciences 118 (40), e2107968118, 2021
282021
Structural basis for recognition of N-formyl peptides as pathogen-associated molecular patterns
G Chen, X Wang, Q Liao, Y Ge, H Jiao, Q Chen, Y Liu, W Lyu, L Zhu, ...
Nature communications 13 (1), 5232, 2022
232022
Structural basis of GM-CSF and IL-2 sequestration by the viral decoy receptor GIF
J Felix, E Kandiah, S De Munck, Y Bloch, GC Van Zundert, K Pauwels, ...
Nature Communications 7 (1), 13228, 2016
212016
Defining the limits and reliability of rigid-body fitting in cryo-EM maps using multi-scale image pyramids
GCP Van Zundert, A Bonvin
Journal of Structural Biology 195 (2), 252-258, 2016
122016
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