Geerke DP - Search Results

1

Polarisable force fields: what do they add in biomolecular simulations?

Inakollu VS, Geerke DP, Rowley CN, Yu H. Inakollu VS, et al. Among authors: geerke dp. Curr Opin Struct Biol. 2020 Apr;61:182-190. doi: 10.1016/j.sbi.2019.12.012. Epub 2020 Feb 8. Curr Opin Struct Biol. 2020. PMID: 32044671 Review.

2

Biomolecular modeling: Goals, problems, perspectives.

van Gunsteren WF, Bakowies D, Baron R, Chandrasekhar I, Christen M, Daura X, Gee P, Geerke DP, Glättli A, Hünenberger PH, Kastenholz MA, Oostenbrink C, Schenk M, Trzesniak D, van der Vegt NF, Yu HB. van Gunsteren WF, et al. Among authors: geerke dp. Angew Chem Int Ed Engl. 2006 Jun 19;45(25):4064-92. doi: 10.1002/anie.200502655. Angew Chem Int Ed Engl. 2006. PMID: 16761306 Review.

3

Molecular dynamics simulations of liquid methanol and methanol-water mixtures with polarizable models.

Yu H, Geerke DP, Liu H, van Gunsteren WF. Yu H, et al. Among authors: geerke dp. J Comput Chem. 2006 Oct;27(13):1494-504. doi: 10.1002/jcc.20429. J Comput Chem. 2006. PMID: 16838298

4

Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.

van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH. van Lipzig MM, et al. J Med Chem. 2004 Feb 12;47(4):1018-30. doi: 10.1021/jm0309607. J Med Chem. 2004. PMID: 14761204

5

Charge group partitioning in biomolecular simulation.

Canzar S, El-Kebir M, Pool R, Elbassioni K, Mark AE, Geerke DP, Stougie L, Klau GW. Canzar S, et al. Among authors: geerke dp. J Comput Biol. 2013 Mar;20(3):188-98. doi: 10.1089/cmb.2012.0239. J Comput Biol. 2013. PMID: 23461571 Free PMC article.

6

CYP 2D6 binding affinity predictions using multiple ligand and protein conformations.

Perić-Hassler L, Stjernschantz E, Oostenbrink C, Geerke DP. Perić-Hassler L, et al. Among authors: geerke dp. Int J Mol Sci. 2013 Dec 17;14(12):24514-30. doi: 10.3390/ijms141224514. Int J Mol Sci. 2013. PMID: 24351831 Free PMC article.

7

Towards automated binding affinity prediction using an iterative linear interaction energy approach.

Vosmeer CR, Pool R, Van Stee MF, Peric-Hassler L, Vermeulen NP, Geerke DP. Vosmeer CR, et al. Among authors: geerke dp. Int J Mol Sci. 2014 Jan 9;15(1):798-816. doi: 10.3390/ijms15010798. Int J Mol Sci. 2014. PMID: 24413750 Free PMC article.

8

Linear Interaction Energy Based Prediction of Cytochrome P450 1A2 Binding Affinities with Reliability Estimation.

Capoferri L, Verkade-Vreeker MC, Buitenhuis D, Commandeur JN, Pastor M, Vermeulen NP, Geerke DP. Capoferri L, et al. Among authors: geerke dp. PLoS One. 2015 Nov 9;10(11):e0142232. doi: 10.1371/journal.pone.0142232. eCollection 2015. PLoS One. 2015. PMID: 26551865 Free PMC article.

9

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. Among authors: geerke dp. 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.

10

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: geerke dp. 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.

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