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Primer for Designing Main Protease (M^pro) Inhibitors of SARS-CoV-2.

Thakur A, Sharma G, Badavath VN, Jayaprakash V, Merz KM Jr, Blum G, Acevedo O. Thakur A, et al. Among authors: merz km jr. J Phys Chem Lett. 2022 Jun 21;13(25):5776-5786. doi: 10.1021/acs.jpclett.2c01193. Online ahead of print. J Phys Chem Lett. 2022. PMID: 35726889 Free PMC article.

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A Polarizable Cationic Dummy Metal Ion Model.

Rahnamoun A, O'Hearn KA, Kaymak MC, Li Z, Merz KM Jr, Aktulga HM. Rahnamoun A, et al. Among authors: merz km jr. J Phys Chem Lett. 2022 Jun 8:5334-5340. doi: 10.1021/acs.jpclett.2c01279. Online ahead of print. J Phys Chem Lett. 2022. PMID: 35675715

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Systematic Evaluation of Ion Diffusion and Water Exchange.

Li Z, Merz KM Jr. Li Z, et al. Among authors: merz km jr. J Chem Theory Comput. 2022 May 10;18(5):3017-3026. doi: 10.1021/acs.jctc.1c01189. Epub 2022 Apr 14. J Chem Theory Comput. 2022. PMID: 35420428 Free PMC article.

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In Silico Collision Cross Section Calculations to Aid Metabolite Annotation.

Das S, Tanemura KA, Dinpazhoh L, Keng M, Schumm C, Leahy L, Asef CK, Rainey M, Edison AS, Fernández FM, Merz KM Jr. Das S, et al. Among authors: merz km jr. J Am Soc Mass Spectrom. 2022 May 4;33(5):750-759. doi: 10.1021/jasms.1c00315. Epub 2022 Apr 4. J Am Soc Mass Spectrom. 2022. PMID: 35378036

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FFENCODER-PL: Pair Wise Energy Descriptors for Protein-Ligand Pose Selection.

Pei J, Song LF, Merz KM Jr. Pei J, et al. Among authors: merz km jr. J Chem Theory Comput. 2021 Oct 12;17(10):6647-6657. doi: 10.1021/acs.jctc.1c00503. Epub 2021 Sep 23. J Chem Theory Comput. 2021. PMID: 34553938

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Correction to "Parameterization of Monovalent Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models".

Sengupta A, Li Z, Song LF, Li P, Merz KM Jr. Sengupta A, et al. Among authors: merz km jr. J Chem Inf Model. 2021 Jul 26;61(7):3734-3735. doi: 10.1021/acs.jcim.1c00576. Epub 2021 Jun 28. J Chem Inf Model. 2021. PMID: 34180237 No abstract available.

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Harnessing the Power of Multi-GPU Acceleration into the Quantum Interaction Computational Kernel Program.

Manathunga M, Jin C, Cruzeiro VWD, Miao Y, Mu D, Arumugam K, Keipert K, Aktulga HM, Merz KM Jr, Götz AW. Manathunga M, et al. Among authors: merz km jr. J Chem Theory Comput. 2021 Jul 13;17(7):3955-3966. doi: 10.1021/acs.jctc.1c00145. Epub 2021 Jun 1. J Chem Theory Comput. 2021. PMID: 34062061

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Quantum Chemistry Calculations for Metabolomics.

Borges RM, Colby SM, Das S, Edison AS, Fiehn O, Kind T, Lee J, Merrill AT, Merz KM Jr, Metz TO, Nunez JR, Tantillo DJ, Wang LP, Wang S, Renslow RS. Borges RM, et al. Among authors: merz km jr. Chem Rev. 2021 May 26;121(10):5633-5670. doi: 10.1021/acs.chemrev.0c00901. Epub 2021 May 12. Chem Rev. 2021. PMID: 33979149 Free PMC article. Review.

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Open-Source Multi-GPU-Accelerated QM/MM Simulations with AMBER and QUICK.

Cruzeiro VWD, Manathunga M, Merz KM Jr, Götz AW. Cruzeiro VWD, et al. Among authors: merz km jr. J Chem Inf Model. 2021 May 24;61(5):2109-2115. doi: 10.1021/acs.jcim.1c00169. Epub 2021 Apr 29. J Chem Inf Model. 2021. PMID: 33913331

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Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.

Li Z, Song LF, Li P, Merz KM Jr. Li Z, et al. Among authors: merz km jr. J Chem Theory Comput. 2021 Apr 13;17(4):2342-2354. doi: 10.1021/acs.jctc.0c01320. Epub 2021 Apr 1. J Chem Theory Comput. 2021. PMID: 33793233 Free PMC article.

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