Anton Feenstra

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Jaap HeringaProfessor of Bioinformatics, Vrije Universiteit AmsterdamVerified email at vu.nl
Sanne AbelnProfessor of AI Technology for Life, Utrecht UniversityVerified email at uu.nl
David van der SpoelProfessor of Biology, Uppsala UniversityVerified email at xray.bmc.uu.se
Erik LindahlProfessor of Biophysics, Linköping UniversityVerified email at liu.se
Berk HessKTH Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Stockholm, SwedenVerified email at scilifelab.se
NPE VermeulenHoogleraar VUVerified email at vu.nl
Walter PirovanoResearch project manager, gut-brain axis enthusiast, VU UniversityVerified email at vu.nl
D. Peter TielemanCanada Research Chair in Molecular Simulation, University of CalgaryVerified email at ucalgary.ca
Qingzhen Hou3BIO-BioInfo - BioModeling, BioInformatics & BioProcesses, Université Libre de BruxellesVerified email at ulb.ac.be
Pieter MeulenhoffTNOVerified email at tno.nl
Nicola BonzanniVU University AmsterdamVerified email at vu.nl
Chris de GraafStructure TherapeuticsVerified email at structuretx.com
Annika JacobsenBioSemantics Group, Human Genetics, Leiden University Medical CenterVerified email at lumc.nl
Wan FokkinkProfessor of Computer Science, Vrije Universiteit AmsterdamVerified email at vu.nl
Mark AbrahamVoxo ABVerified email at kth.se
Alan E. MarkProfessor of Biophysical Chemistry, University of QueenslandVerified email at uq.edu.au
Ting LiuGongli Hospital of Shanghai Pudong New AreaVerified email at glhospital.com
Zhisheng HuangSenior Researcher of Computer Science, Vrije University AmsterdamVerified email at cs.vu.nl
Elzbieta KrepskaVU University AmsterdamVerified email at vu.nl
Punto BawonoThe Centre for Integrative Bioinformatics VU (IBIVU)Verified email at vu.nl

Anton Feenstra

Assistant professor of Bioinformatics, IBIVU Centre for Integrative Bioinformatics, VU University

Verified email at vu.nl - Homepage

Bioinformatics Protein-protein interactions Modelling signalling and regulation in biological cells Petri net modelling


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Improving efficiency of large timescale molecular dynamics simulations of hydrogen-rich systems KA Feenstra, B Hess, HJC Berendsen J Comput Chem 20, 786-798, 1999	1027	1999
Gromacs User Manual version 4.0, 2005 D Van Der Spoel, E Lindahl, B Hess, AR Van Buuren, E Apol, ... URL http://www. gromacs. org/Documentation/Manual, 2009	910*	2009
GROMACS user manual version 5.1 MJ Abraham, D Van Der Spoel, E Lindahl, B Hess	620*	2014
Cytochrome P450 in silico: an integrative modeling approach C De Graaf, NPE Vermeulen, KA Feenstra Journal of medicinal chemistry 48 (8), 2725-2755, 2005	287	2005
Dynamic conformations of flavin adenine dinucleotide: simulated molecular dynamics of the flavin cofactor related to the time-resolved fluorescence characteristics PAW Van den Berg, KA Feenstra, AE Mark, HJC Berendsen, AJWG Visser The Journal of Physical Chemistry B 106 (34), 8858-8869, 2002	189	2002
Interaction of 14-3-3 proteins with the estrogen receptor alpha F domain provides a drug target interface IJ De Vries-van Leeuwen, D da Costa Pereira, KD Flach, SR Piersma, ... Proceedings of the National Academy of Sciences 110 (22), 8894-8899, 2013	151	2013
PRALINE™: a strategy for improved multiple alignment of transmembrane proteins W Pirovano, KA Feenstra, J Heringa Bioinformatics 24 (4), 492-497, 2008	141	2008
Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting K Ye, K Anton Feenstra, J Heringa, AP IJzerman, E Marchiori Bioinformatics 24 (1), 18-25, 2008	100	2008
Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model N Bonzanni, A Garg, KA Feenstra, J Schütte, S Kinston, ... Bioinformatics 29 (13), i80-i88, 2013	94	2013
Sequence comparison by sequence harmony identifies subtype-specific functional sites W Pirovano, KA Feenstra, J Heringa Nucleic acids research 34 (22), 6540-6548, 2006	85	2006
Seeing the trees through the forest: sequence-based homo-and heteromeric protein-protein interaction sites prediction using random forest Q Hou, PFG De Geest, WF Vranken, J Heringa, KA Feenstra Bioinformatics 33 (10), 1479-1487, 2017	81	2017
Metabolic Regio- and Stereoselectivity of Cytochrome P450 2D6 towards 3,4-Methylenedioxy-N-alkylamphetamines: in Silico Predictions and Experimental … PHJ Keizers, C de Graaf, FJJ de Kanter, C Oostenbrink, KA Feenstra, ... Journal of medicinal chemistry 48 (19), 6117-6127, 2005	79	2005
Altering the regioselectivity of cytochrome P450 CYP102A3 of Bacillus subtilis by using a new versatile assay system O Lentz, A Feenstra, T Habicher, B Hauer, RD Schmid, VB Urlacher ChemBioChem 7 (2), 345-350, 2006	75	2006
Multi-Harmony: detecting functional specificity from sequence alignment BW Brandt, KA Feenstra, J Heringa Nucleic acids research 38 (suppl_2), W35-W40, 2010	72	2010
The potential use of big data in oncology SM Willems, S Abeln, KA Feenstra, R de Bree, EF van der Poel, ... Oral oncology 98, 8-12, 2019	70	2019
Multiple sequence alignment P Bawono, M Dijkstra, W Pirovano, A Feenstra, S Abeln, J Heringa Bioinformatics: volume I: data, sequence analysis, and evolution, 167-189, 2017	65	2017
Executing multicellular differentiation: quantitative predictive modelling of C.elegans vulval development N Bonzanni, E Krepska, KA Feenstra, W Fokkink, T Kielmann, H Bal, ... Bioinformatics 25 (16), 2049-2056, 2009	62	2009
Aurora kinase A (AURKA) interaction with Wnt and Ras-MAPK signalling pathways in colorectal cancer A Jacobsen, LJW Bosch, SR Martens-de Kemp, B Carvalho, ... Scientific reports 8 (1), 7522, 2018	59	2018
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins A May, R Pool, E van Dijk, J Bijlard, S Abeln, J Heringa, KA Feenstra Bioinformatics 30 (3), 326-334, 2014	58	2014
Gromacs User Manual version 3.0, Nijenborgh 4, 9747 AG Groningen, The Netherlands D van der Spoel, AR van Buuren, E Apol, PJ Meulenhoff, DP Tieleman, ... Internet: http://www. gromacs. org, 2001	56	2001

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