Khalak Y - Search Results

1

Chemical Space Exploration with Active Learning and Alchemical Free Energies.

Khalak Y, Tresadern G, Hahn DF, de Groot BL, Gapsys V. Khalak Y, et al. J Chem Theory Comput. 2022 Oct 11;18(10):6259-6270. doi: 10.1021/acs.jctc.2c00752. Epub 2022 Sep 23. J Chem Theory Comput. 2022. PMID: 36148968 Free PMC article.

2

Alchemical absolute protein-ligand binding free energies for drug design.

Khalak Y, Tresadern G, Aldeghi M, Baumann HM, Mobley DL, de Groot BL, Gapsys V. Khalak Y, et al. Chem Sci. 2021 Sep 24;12(41):13958-13971. doi: 10.1039/d1sc03472c. eCollection 2021 Oct 27. Chem Sci. 2021. PMID: 34760182 Free PMC article.

3

Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software.

Khalak Y, Tresadern G, de Groot BL, Gapsys V. Khalak Y, et al. J Comput Aided Mol Des. 2021 Jan;35(1):49-61. doi: 10.1007/s10822-020-00359-1. Epub 2020 Nov 24. J Comput Aided Mol Des. 2021. PMID: 33230742 Free PMC article.

4

Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTP.

Wehner J, Brombacher L, Brown J, Junghans C, Çaylak O, Khalak Y, Madhikar P, Tirimbò G, Baumeier B. Wehner J, et al. Among authors: khalak y. J Chem Theory Comput. 2018 Dec 11;14(12):6253-6268. doi: 10.1021/acs.jctc.8b00617. Epub 2018 Nov 21. J Chem Theory Comput. 2018. PMID: 30404449 Free PMC article.

5

Improved general-purpose five-point model for water: TIP5P/2018.

Khalak Y, Baumeier B, Karttunen M. Khalak Y, et al. J Chem Phys. 2018 Dec 14;149(22):224507. doi: 10.1063/1.5070137. J Chem Phys. 2018. PMID: 30553255

6

Non-conformal coarse-grained potentials for water.

Rodríguez-López T, Khalak Y, Karttunen M. Rodríguez-López T, et al. Among authors: khalak y. J Chem Phys. 2017 Oct 7;147(13):134108. doi: 10.1063/1.4985914. J Chem Phys. 2017. PMID: 28987109

7

Accurate absolute free energies for ligand-protein binding based on non-equilibrium approaches.

Gapsys V, Yildirim A, Aldeghi M, Khalak Y, van der Spoel D, de Groot BL. Gapsys V, et al. Among authors: khalak y. Commun Chem. 2021 May 11;4(1):61. doi: 10.1038/s42004-021-00498-y. Commun Chem. 2021. PMID: 36697634 Free PMC article.

8

Redefining the minimal substrate tolerance of mandelate racemase. Racemization of trifluorolactate.

Nagar M, Narmandakh A, Khalak Y, Bearne SL. Nagar M, et al. Among authors: khalak y. Biochemistry. 2011 Oct 18;50(41):8846-52. doi: 10.1021/bi201188j. Epub 2011 Sep 21. Biochemistry. 2011. PMID: 21894901

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