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- Kenno Vanommeslaeghe, Elizabeth Hatcher, +8 authors Alexander D. MacKerell
- Journal of Computational Chemistry
- 2009
The widely used CHARMM additive all-atom force field includes parameters for proteins, nucleic acids, lipids, and carbohydrates. In the present article, an extension of the CHARMM force field to… (More)
- Robert B. Best, Xiao Zhu, +4 authors Alexander D. MacKerell
- Journal of chemical theory and computation
- 2012
While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the model with respect to the equilibrium… (More)
- Miguel Fribourg, José L. Moreno, +19 authors Diomedes E. Logothetis
- Cell
- 2011
Atypical antipsychotic drugs, such as clozapine and risperidone, have a high affinity for the serotonin 5-HT(2A) G protein-coupled receptor (GPCR), the 2AR, which signals via a G(q) heterotrimeric G… (More)
- Jason R. Healy, Padmavani Bezawada, +5 authors Rae R. Matsumoto
- ACS chemical neuroscience
- 2013
Opioid narcotics are used for the treatment of moderate-to-severe pain and primarily exert their analgesic effects through μ receptors. Although traditional μ agonists can cause undesired side… (More)
- Pedro E. M. Lopes, Jing Huang, +4 authors Alexander D. MacKerell
- Journal of chemical theory and computation
- 2013
Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and molecular dynamics (MD) simulation… (More)
- Jihyun Shim, Alexander D. MacKerell
- MedChemComm
- 2011
A significant number of drug discovery efforts are based on natural products or high throughput screens from which compounds showing potential therapeutic effects are identified without knowledge of… (More)
- Jihyun Shim, Andrew Coop, Alexander D. MacKerell
- The journal of physical chemistry. B
- 2013
Molecular details of μ opioid receptor activations were obtained using molecular dynamics simulations of the receptor in the presence of three agonists, three antagonists, and a partial agonist and… (More)
- Jihyun Shim, Andrew Coop, Alexander D. MacKerell
- The journal of physical chemistry. B
- 2011
Despite being studied for over 30 years, a consensus structure-activity relationship (SAR) that encompasses the full range peptidic and nonpeptidic μ-opioid receptor ligands is still not available.… (More)
- Xiao Zhu, Pedro E. M. Lopes, Jihyun Shim, Alexander D. MacKerell
- Journal of Chemical Information and Modeling
- 2012
Amino acid side-chain conformational properties influence the overall structural and dynamic properties of proteins and, therefore, their biological functions. In this study, quantum mechanical (QM)… (More)
- Mihye Lee, Jihyun Shim, Philjae Kang, Ilia A Guzei, Soo Hyuk Choi
- Angewandte Chemie
- 2013
The development of proteinlike structures of oligomers which contain unnatural amino acids (peptidic foldamers) is an active area of research. A variety of distinct conformations of peptidic… (More)