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Aalt D.J. van Dijk
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A large-scale evaluation of computational protein function prediction
P Radivojac, WT Clark, TR Oron, AM Schnoes, T Wittkop, A Sokolov, ...
Nature methods 10 (3), 221-227, 2013
8902013
HADDOCK versus HADDOCK: new features and performance of HADDOCK2. 0 on the CAPRI targets
SJ De Vries, ADJ Van Dijk, M Krzeminski, M van Dijk, A Thureau, V Hsu, ...
Proteins: structure, function, and bioinformatics 69 (4), 726-733, 2007
6462007
An expanded evaluation of protein function prediction methods shows an improvement in accuracy
Y Jiang, TR Oron, WT Clark, AR Bankapur, D D’Andrea, R Lepore, ...
Genome biology 17 (1), 1-19, 2016
3412016
Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis
Y Zhang, ADJ Van Dijk, A Scaffidi, GR Flematti, M Hofmann, ...
Nature chemical biology 10 (12), 1028-1033, 2014
3002014
SEPALLATA3: the'glue'for MADS box transcription factor complex formation
RGH Immink, IAN Tonaco, S de Folter, A Shchennikova, ADJ van Dijk, ...
Genome biology 10 (2), 1-16, 2009
2722009
Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically
S Danisman, F Van der Wal, S Dhondt, R Waites, S de Folter, A Bimbo, ...
Plant physiology 159 (4), 1511-1523, 2012
2532012
Data‐driven docking for the study of biomolecular complexes
ADJ Van Dijk, R Boelens, AMJJ Bonvin
The FEBS journal 272 (2), 293-312, 2005
2062005
Information-driven protein–DNA docking using HADDOCK: it is a matter of flexibility
M van Dijk, ADJ van Dijk, V Hsu, R Boelens, AMJJ Bonvin
Nucleic acids research 34 (11), 3317-3325, 2006
1972006
Characterization of SOC1’s central role in flowering by the identification of its upstream and downstream regulators
RGH Immink, D PosÚ, S Ferrario, F Ott, K Kaufmann, FL Valentim, ...
Plant physiology 160 (1), 433-449, 2012
1902012
WHISCY: what information does surface conservation yield? Application to data‐driven docking
SJ de Vries, ADJ van Dijk, AMJJ Bonvin
Proteins: Structure, Function, and Bioinformatics 63 (3), 479-489, 2006
1752006
Solvated docking: introducing water into the modelling of biomolecular complexes
ADJ Van Dijk, AMJJ Bonvin
Bioinformatics 22 (19), 2340-2347, 2006
1612006
Towards recommendations for metadata and data handling in plant phenotyping
P Krajewski, D Chen, H Ćwiek, ADJ van Dijk, F Fiorani, P Kersey, ...
Journal of Experimental Botany 66 (18), 5417-5427, 2015
1202015
Bayesian Markov Random Field analysis for protein function prediction based on network data
YAI Kourmpetis, ADJ Van Dijk, MCAM Bink, RCHJ van Ham, ...
PloS one 5 (2), e9293, 2010
1152010
Data‐driven docking: HADDOCK's adventures in CAPRI
ADJ Van Dijk, SJ De Vries, C Dominguez, H Chen, HX Zhou, A Bonvin
Proteins: Structure, Function, and Bioinformatics 60 (2), 232-238, 2005
1082005
Valencene synthase from the heartwood of Nootka cypress (Callitropsis nootkatensis) for biotechnological production of valencene
J Beekwilder, A van Houwelingen, K Cankar, ADJ van Dijk, RM de Jong, ...
Plant biotechnology journal 12 (2), 174-182, 2014
1072014
Analysis of functional redundancies within the Arabidopsis TCP transcription factor family
S Danisman, ADJ van Dijk, A Bimbo, F van der Wal, L Hennig, S de Folter, ...
Journal of experimental botany 64 (18), 5673-5685, 2013
1022013
The (r)evolution of gene regulatory networks controlling Arabidopsis plant reproduction: a two-decade history
A Pajoro, S Biewers, E Dougali, F Leal Valentim, MA Mendes, A Porri, ...
Journal of Experimental Botany 65 (17), 4731-4745, 2014
982014
Various strategies of using residual dipolar couplings in NMR‐driven protein docking: Application to Lys48‐linked di‐ubiquitin and validation against 15Ná…
ADJ van Dijk, D Fushman, AMJJ Bonvin
Proteins: Structure, Function, and Bioinformatics 60 (3), 367-381, 2005
982005
N-glycan occupancy of Arabidopsis N-glycoproteins
W Song, RA Mentink, MGL Henquet, JHG Cordewener, ADJ van Dijk, ...
Journal of proteomics 93, 343-355, 2013
712013
Cross-family transcription factor interactions: an additional layer of gene regulation
M Bemer, ADJ van Dijk, RGH Immink, GC Angenent
Trends in plant science 22 (1), 66-80, 2017
702017
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Articles 1–20