MacKerell AD Jr - Search Results

1

Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme.

Baral P, Sengul MY, MacKerell AD Jr. Baral P, et al. Among authors: mackerell ad jr. J Chem Phys. 2024 Dec 14;161(22):225102. doi: 10.1063/5.0241246. J Chem Phys. 2024. PMID: 39665326

2

Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities.

Kumar A, Goel H, Yu W, Zhao M, MacKerell AD Jr. Kumar A, et al. Among authors: mackerell ad jr. J Chem Theory Comput. 2024 Dec 24;20(24):11032-11048. doi: 10.1021/acs.jctc.4c01165. Epub 2024 Dec 5. J Chem Theory Comput. 2024. PMID: 39636837

3

Isolation of phytoconstituents from an extract of Murraya paniculata with cytotoxicity and antioxidant activities and in silico evaluation of their potential to bind to aldose reductase (AKR1B1).

Shanta AP, Fatema-Tuz-Zohora, Mahtarin R, MacKerell AD Jr, Ahsan M. Shanta AP, et al. Among authors: mackerell ad jr. J Biomol Struct Dyn. 2024 Dec 5:1-15. doi: 10.1080/07391102.2024.2435623. Online ahead of print. J Biomol Struct Dyn. 2024. PMID: 39636240

4

Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.

Nan Y, Baral P, Orr AA, Michel HM, Lemkul JA, MacKerell AD Jr. Nan Y, et al. Among authors: mackerell ad jr. J Phys Chem B. 2024 Dec 12;128(49):12078-12091. doi: 10.1021/acs.jpcb.4c06354. Epub 2024 Dec 3. J Phys Chem B. 2024. PMID: 39625472

5

Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.

Teng X, Yu W, MacKerell AD Jr. Teng X, et al. Among authors: mackerell ad jr. J Chem Theory Comput. 2024 Nov 26;20(22):10034-10044. doi: 10.1021/acs.jctc.4c00966. Epub 2024 Nov 13. J Chem Theory Comput. 2024. PMID: 39536452

6

Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.

J N C, Guvench O, MacKerell AD Jr, Yamaguchi T, Mallajosyula SS. J N C, et al. Among authors: mackerell ad jr. J Chem Theory Comput. 2024 Oct 22;20(20):9161-9177. doi: 10.1021/acs.jctc.4c00656. Epub 2024 Oct 9. J Chem Theory Comput. 2024. PMID: 39383338

7

Exploring Druggable Binding Sites on the Class A GPCRs Using the Residue Interaction Network and Site Identification by Ligand Competitive Saturation.

Inan T, Yuce M, MacKerell AD Jr, Kurkcuoglu O. Inan T, et al. Among authors: mackerell ad jr. ACS Omega. 2024 Sep 13;9(38):40154-40171. doi: 10.1021/acsomega.4c06172. eCollection 2024 Sep 24. ACS Omega. 2024. PMID: 39346853 Free PMC article.

8

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.

Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, Deng Y, Devereux M, Ding X, Feig MF, Gao J, Glowacki DR, Gonzales JE 2nd, Hamaneh MB, Harder ED, Hayes RL, Huang J, Huang Y, Hudson PS, Im W, Islam SM, Jiang W, Jones MR, Käser S, Kearns FL, Kern NR, Klauda JB, Lazaridis T, Lee J, Lemkul JA, Liu X, Luo Y, MacKerell AD Jr, Major DT, Meuwly M, Nam K, Nilsson L, Ovchinnikov V, Paci E, Park S, Pastor RW, Pittman AR, Post CB, Prasad S, Pu J, Qi Y, Rathinavelan T, Roe DR, Roux B, Rowley CN, Shen J, Simmonett AC, Sodt AJ, Töpfer K, Upadhyay M, van der Vaart A, Vazquez-Salazar LI, Venable RM, Warrensford LC, Woodcock HL, Wu Y, Brooks CL 3rd, Brooks BR, Karplus M. Hwang W, et al. Among authors: mackerell ad jr. J Phys Chem B. 2024 Oct 17;128(41):9976-10042. doi: 10.1021/acs.jpcb.4c04100. Epub 2024 Sep 20. J Phys Chem B. 2024. PMID: 39303207 Free PMC article. Review.

9

First-in-Class Mitogen-Activated Protein Kinase p38α: MAPK-Activated Protein Kinase-2 (MK2) Dual Signal Modulator with Anti-inflammatory and Endothelial-stabilizing Properties.

Tulapurkar ME, Shirey KA, Lugkey KN, Luo W, Lal R, Galan A, Mahmoud O, McClean N, Thangaraju K, Cericola D, Lewis D, Murphy WA, Fletcher S, MacKerell AD Jr, Vogel SN, Shapiro P, Hasday JD. Tulapurkar ME, et al. Among authors: mackerell ad jr. J Pharmacol Exp Ther. 2024 Sep 16:JPET-AR-2024-002281. doi: 10.1124/jpet.124.002281. Online ahead of print. J Pharmacol Exp Ther. 2024. PMID: 39284624 Free article.

10

Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.

Nordquist EB, Zhao M, Kumar A, MacKerell AD Jr. Nordquist EB, et al. Among authors: mackerell ad jr. J Chem Inf Model. 2024 Oct 14;64(19):7743-7757. doi: 10.1021/acs.jcim.4c01189. Epub 2024 Sep 16. J Chem Inf Model. 2024. PMID: 39283165

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