Alexander D MacKerell Jr
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Explore the profile of Alexander D MacKerell Jr including associated specialties, affiliations and a list of published articles.
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Recent Articles
1.
Croitoru A, Kumar A, Lambry J, Lee J, Sharif S, Yu W, et al.
J Chem Theory Comput
. 2025 Mar;
PMID: 40033678
Small molecule empirical force fields (FFs), including the CHARMM General Force Field (CGenFF), are designed to have wide coverage of organic molecules and to rapidly assign parameters to molecules not...
2.
Li X, Orr A, Sajadi M, DeVico A, Deredge D, MacKerell Jr A, et al.
Mol Pharm
. 2025 Mar;
PMID: 40029670
N49P9.6-FR-LS and PGT121 are promising antibodies with significant therapeutic potential against HIV infection, but they are prone to precipitation at concentrations greater than 12 to 13 mg/mL. This study evaluates...
3.
Tulapurkar M, Shirey K, Lugkey K, Luo W, Lal R, Galan A, et al.
J Pharmacol Exp Ther
. 2025 Feb;
392(3):100031.
PMID: 39969269
We previously identified a small molecule, UM101, predicted to bind to the substrate-binding groove of p38α mitogen-activated protein kinase (MAPK) near the binding site of its proinflammatory substrate, mitogen-activated protein...
4.
Teng X, Yu W, MacKerell Jr A
J Phys Chem Lett
. 2025 Jan;
16(4):1016-1023.
PMID: 39841123
An improvement in the computational efficiency of polarizable force field simulations is made through the development of a polarizable Drude water model, SWM3, in combination with the use of Lennard-Jones...
5.
Yu W, Weber D, MacKerell Jr A
J Chem Inf Model
. 2024 Dec;
PMID: 39729368
Drug efficacy often correlates better with dissociation kinetics than binding affinity alone. To study binding kinetics computationally, it is necessary to identify all of the possible ligand dissociation pathways. The...
6.
Baral P, Sengul M, MacKerell Jr A
J Chem Phys
. 2024 Dec;
161(22).
PMID: 39665326
Molecular dynamics simulations are crucial for understanding the structural and dynamical behavior of biomolecular systems, including the impact of their environment. However, there is a gap between the time scale...
7.
Kumar A, Goel H, Yu W, Zhao M, MacKerell Jr A
J Chem Theory Comput
. 2024 Dec;
20(24):11032-11048.
PMID: 39636837
Appropriate treatment of water contributions to protein-ligand interactions is a very challenging problem in the context of adequately determining the number of waters to investigate and undertaking conformational sampling of...
8.
Shanta A, Fatema-Tuz-Zohora , Mahtarin R, MacKerell Jr A, Ahsan M
J Biomol Struct Dyn
. 2024 Dec;
:1-15.
PMID: 39636240
The study on (Orange Jasmine) stem bark extract found it to have antioxidant and cytotoxic proper-ties. The structures of the isolated phytoconstituents were determined using NMR spectroscopy. Compounds were evaluated...
9.
Nan Y, Baral P, Orr A, Michel H, Lemkul J, MacKerell Jr A
J Phys Chem B
. 2024 Dec;
128(49):12078-12091.
PMID: 39625472
An accurate force field (FF) is the foundation of reliable results from molecular dynamics (MD) simulations. In our recently published work, we developed a protocol to generate atom pair-specific Lennard-Jones...
10.
Teng X, Yu W, MacKerell Jr A
J Chem Theory Comput
. 2024 Nov;
20(22):10034-10044.
PMID: 39536452
In this work the 4-point polarizable SWM4 Drude water model is reparametrized. Multiple models were developed using different strategies toward reproduction of specific target data. Results indicate that no individual...