van Dijk M - Search Results

1

OFraMP: a fragment-based tool to facilitate the parametrization of large molecules.

Stroet M, Caron B, Engler MS, van der Woning J, Kauffmann A, van Dijk M, El-Kebir M, Visscher KM, Holownia J, Macfarlane C, Bennion BJ, Gelpi-Dominguez S, Lightstone FC, van der Storm T, Geerke DP, Mark AE, Klau GW. Stroet M, et al. Among authors: van der woning j, van der storm t, van dijk m. J Comput Aided Mol Des. 2023 Aug;37(8):357-371. doi: 10.1007/s10822-023-00511-7. Epub 2023 Jun 13. J Comput Aided Mol Des. 2023. PMID: 37310542 Free PMC article.

2

Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2.

Rifai EA, van Dijk M, Vermeulen NPE, Geerke DP. Rifai EA, et al. Among authors: van dijk m. J Comput Aided Mol Des. 2018 Jan;32(1):239-249. doi: 10.1007/s10822-017-0055-0. Epub 2017 Sep 9. J Comput Aided Mol Des. 2018. PMID: 28889350 Free PMC article.

3

Recent Developments in Linear Interaction Energy Based Binding Free Energy Calculations.

Rifai EA, van Dijk M, Geerke DP. Rifai EA, et al. Among authors: van dijk m. Front Mol Biosci. 2020 Jun 17;7:114. doi: 10.3389/fmolb.2020.00114. eCollection 2020. Front Mol Biosci. 2020. PMID: 32626725 Free PMC article.

4

Comprehensive and Automated Linear Interaction Energy Based Binding-Affinity Prediction for Multifarious Cytochrome P450 Aromatase Inhibitors.

van Dijk M, Ter Laak AM, Wichard JD, Capoferri L, Vermeulen NPE, Geerke DP. van Dijk M, et al. J Chem Inf Model. 2017 Sep 25;57(9):2294-2308. doi: 10.1021/acs.jcim.7b00222. Epub 2017 Aug 23. J Chem Inf Model. 2017. PMID: 28776988 Free PMC article.

5

eTOX ALLIES: an automated pipeLine for linear interaction energy-based simulations.

Capoferri L, van Dijk M, Rustenburg AS, Wassenaar TA, Kooi DP, Rifai EA, Vermeulen NPE, Geerke DP. Capoferri L, et al. Among authors: van dijk m. J Cheminform. 2017 Nov 21;9(1):58. doi: 10.1186/s13321-017-0243-x. J Cheminform. 2017. PMID: 29159598 Free PMC article.

6

A Comparative Linear Interaction Energy and MM/PBSA Study on SIRT1-Ligand Binding Free Energy Calculation.

Rifai EA, van Dijk M, Vermeulen NPE, Yanuar A, Geerke DP. Rifai EA, et al. Among authors: van dijk m. J Chem Inf Model. 2019 Sep 23;59(9):4018-4033. doi: 10.1021/acs.jcim.9b00609. Epub 2019 Sep 11. J Chem Inf Model. 2019. PMID: 31461271 Free PMC article.

7

Solvated protein-DNA docking using HADDOCK.

van Dijk M, Visscher KM, Kastritis PL, Bonvin AM. van Dijk M, et al. J Biomol NMR. 2013 May;56(1):51-63. doi: 10.1007/s10858-013-9734-x. Epub 2013 Apr 30. J Biomol NMR. 2013. PMID: 23625455

8

Drug toxicity profiling of a Saccharomyces cerevisiae deubiquitinase deletion panel shows that acetaminophen mimics tyrosine.

Huseinovic A, van Dijk M, Vermeulen NPE, van Leeuwen F, Kooter JM, Vos JC. Huseinovic A, et al. Among authors: van leeuwen f, van dijk m. Toxicol In Vitro. 2018 Mar;47:259-268. doi: 10.1016/j.tiv.2017.12.007. Epub 2017 Dec 16. Toxicol In Vitro. 2018. PMID: 29258884 Free article.

9

Inter-individual Variability in Activity of the Major Drug Metabolizing Enzymes in Liver Homogenates of 20 Individuals.

den Braver-Sewradj SP, den Braver MW, van Dijk M, Zhang Y, Dekker SJ, Wijaya L, Vermeulen NPE, Richert L, Commandeur JNM, Vos JC. den Braver-Sewradj SP, et al. Among authors: van dijk m. Curr Drug Metab. 2018;19(4):370-381. doi: 10.2174/1389200219666180108160046. Curr Drug Metab. 2018. PMID: 29318967

10

A Flexible, Grid-Enabled Web Portal for GROMACS Molecular Dynamics Simulations.

van Dijk M, Wassenaar TA, Bonvin AM. van Dijk M, et al. J Chem Theory Comput. 2012 Oct 9;8(10):3463-72. doi: 10.1021/ct300102d. Epub 2012 Apr 18. J Chem Theory Comput. 2012. PMID: 26592996

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