CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications

S Feng, S Park, YK Choi, W Im - Journal of chemical theory and …, 2023 - ACS Publications
Molecular dynamics simulations of membranes and membrane proteins serve as
computational microscopes, revealing coordinated events at the membrane interface. As G …

CHARMM at 45: Enhancements in accessibility, functionality, and speed

W Hwang, SL Austin, A Blondel… - The Journal of …, 2024 - ACS Publications
Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

[HTML][HTML] Molecular recognition of morphine and fentanyl by the human μ-opioid receptor

Y Zhuang, Y Wang, B He, X He, XE Zhou, S Guo… - Cell, 2022 - cell.com
Morphine and fentanyl are among the most used opioid drugs that confer analgesia and
unwanted side effects through both G protein and arrestin signaling pathways of μ-opioid …

A single mutation in dairy cow-associated H5N1 viruses increases receptor binding breadth

MR Good, ML Fernández-Quintero, W Ji… - Nature …, 2024 - nature.com
Abstract Clade 2.3. 4.4 b H5N1 is causing an unprecedented outbreak in dairy cows in the
United States. To understand if recent H5N1 viruses are changing their receptor use, we …

CHARMM-GUI PDB manipulator: various PDB structural modifications for biomolecular modeling and simulation

SJ Park, N Kern, T Brown, J Lee, W Im - Journal of molecular biology, 2023 - Elsevier
Molecular modeling and simulation play important roles in biomedical research as they
provide molecular-level insight into the underlying mechanisms of biological functions that …

CHARMM-GUI nanomaterial modeler for modeling and simulation of nanomaterial systems

YK Choi, NR Kern, S Kim, K Kanhaiya… - Journal of chemical …, 2021 - ACS Publications
Molecular modeling and simulation are invaluable tools for nanoscience that predict
mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide …

O-GlcNAcylation promotes pancreatic tumor growth by regulating malate dehydrogenase 1

Q Zhu, H Zhou, L Wu, Z Lai, D Geng, W Yang… - Nature Chemical …, 2022 - nature.com
Oncogenic Kras-activated pancreatic ductal adenocarcinoma (PDAC) cells highly rely on an
unconventional glutamine catabolic pathway to sustain cell growth. However, little is known …

A perspective on sustainable computational chemistry software development and integration

R Di Felice, ML Mayes, RM Richard… - Journal of chemical …, 2023 - ACS Publications
The power of quantum chemistry to predict the ground and excited state properties of
complex chemical systems has driven the development of computational quantum chemistry …

Methotrexate recognition by the human reduced folate carrier SLC19A1

NJ Wright, JG Fedor, H Zhang, P Jeong, Y Suo, J Yoo… - Nature, 2022 - nature.com
Folates are essential nutrients with important roles as cofactors in one-carbon transfer
reactions, being heavily utilized in the synthesis of nucleic acids and the metabolism of …

Structural insights into ligand recognition and activation of the medium-chain fatty acid-sensing receptor GPR84

H Liu, Q Zhang, X He, M Jiang, S Wang, X Yan… - nature …, 2023 - nature.com
GPR84 is an orphan class AG protein-coupled receptor (GPCR) that is predominantly
expressed in immune cells and plays important roles in inflammation, fibrosis, and …