Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model
Lemkul, Justin A., Roux, Benoît, van der Spoel, David, MacKerell Jr, Alexander D.
Published in Journal of computational chemistry (15.07.2015)
Published in Journal of computational chemistry (15.07.2015)
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Journal Article
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data
Huang, Jing, MacKerell Jr, Alexander D.
Published in Journal of computational chemistry (30.09.2013)
Published in Journal of computational chemistry (30.09.2013)
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Journal Article
All-atom polarizable force field for DNA based on the classical drude oscillator model
Savelyev, Alexey, MacKerell Jr, Alexander D.
Published in Journal of computational chemistry (15.06.2014)
Published in Journal of computational chemistry (15.06.2014)
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Journal Article
Optimization of a Benzothiazole Indolene Scaffold Targeting Bacterial Cell Wall Assembly
Chauhan, Jay, Yu, Wenbo, Cardinale, Steven, Opperman, Timothy J, MacKerell, Jr, Alexander D, Fletcher, Steven, de Leeuw, Erik Ph
Published in Drug design, development and therapy (01.02.2020)
Published in Drug design, development and therapy (01.02.2020)
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Journal Article
Development of extracellular signal-regulated kinase inhibitors
Burkhard, Kimberly, Smith, Sarice, Deshmukh, Rahul, MacKerell, Jr, Alexander D, Shapiro, Paul
Published in Current topics in medicinal chemistry (01.05.2009)
Published in Current topics in medicinal chemistry (01.05.2009)
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Journal Article
Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation
Inan, Tugce, Flinko, Robin, Lewis, George K., MacKerell, Alexander D., Kurkcuoglu, Ozge
Published in The journal of physical chemistry. B (30.05.2024)
Published in The journal of physical chemistry. B (30.05.2024)
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Journal Article
Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA
Maiti, Atanu, Noon, Muhammad S, MacKerell, Alexander D. Jr, Pozharski, Edwin, Drohat, Alexander C
Published in Proceedings of the National Academy of Sciences - PNAS (22.05.2012)
Published in Proceedings of the National Academy of Sciences - PNAS (22.05.2012)
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Journal Article
Robustness in the fitting of molecular mechanics parameters
Vanommeslaeghe, Kenno, Yang, Mingjun, MacKerell Jr, Alexander D.
Published in Journal of computational chemistry (30.05.2015)
Published in Journal of computational chemistry (30.05.2015)
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Journal Article
Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy
J N, Chythra, Guvench, Olgun, MacKerell Jr, Alexander D., Yamaguchi, Takumi, Mallajosyula, Sairam S.
Published in Journal of chemical theory and computation (22.10.2024)
Published in Journal of chemical theory and computation (22.10.2024)
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Journal Article
CHARMM36m: an improved force field for folded and intrinsically disordered proteins
Huang, Jing, Rauscher, Sarah, Nawrocki, Grzegorz, Ran, Ting, Feig, Michael, de Groot, Bert L, Grubmüller, Helmut, MacKerell, Alexander D
Published in Nature methods (01.01.2017)
Published in Nature methods (01.01.2017)
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Journal Article
Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA
Denning, Elizabeth J., Priyakumar, U. Deva, Nilsson, Lennart, Mackerell Jr, Alexander D.
Published in Journal of computational chemistry (15.07.2011)
Published in Journal of computational chemistry (15.07.2011)
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Journal Article