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 …

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 …

Nav1.2 channel mutations preventing fast inactivation lead to SCN2A encephalopathy

G Berecki, E Tao, KB Howell, RK Coorg, E Andersen… - Brain, 2025 - academic.oup.com
SCN2A gene-related early-infantile developmental and epileptic encephalopathy (EI-DEE)
is a rare and severe disorder that manifests in early infancy. SCN2A mutations affecting the …

Exploiting in silico structural analysis to introduce emerging genotype–phenotype correlations in DHCR24-related sterol biosynthesis disorder: a case study

D Cocciadiferro, T Mazza, D Vecchio, T Biagini… - Frontiers in …, 2024 - frontiersin.org
Desmosterolosis is a rare sterol biosynthesis disorder characterized by multiple congenital
anomalies, failure to thrive, severe developmental delay, progressive epileptic …

Antiviral drug recognition and elevator-type transport motions of CNT3

NJ Wright, F Zhang, Y Suo, L Kong, Y Yin… - Nature Chemical …, 2024 - nature.com
Nucleoside analogs have broad clinical utility as antiviral drugs. Key to their systemic
distribution and cellular entry are human nucleoside transporters. Here, we establish that the …

Elucidating Protein Structures in the Gas Phase: Traversing Configuration Space with Biasing Methods

VD Gandhi, L Hua, M Lawrenz, M Latif… - Journal of Chemical …, 2024 - ACS Publications
Achieving accurate characterization of protein structures in the gas phase continues to be a
formidable challenge. To tackle this issue, the present study employs Molecular Dynamics …

CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation

L Kong, SJ Park, W Im - Journal of Molecular Biology, 2024 - Elsevier
Molecular modeling and simulation serve an important role in exploring biological functions
of proteins at the molecular level, which is complementary to experiments. CHARMM-GUI …

[HTML][HTML] The Putative Role of TIM-3 Variants in Polyendocrine Autoimmunity: Insights from a WES Investigation

A Ariolli, E Agolini, T Mazza, F Petrizzelli… - International Journal of …, 2024 - mdpi.com
Autoimmune polyglandular syndrome (APS) comprises a complex association of
autoimmune pathological conditions. APS Type 1 originates from loss-of-function mutations …

[HTML][HTML] Analogs of α‐conotoxin PnIC selectively inhibit α7β2‐over α7‐only subtype nicotinic acetylcholine receptors via a novel allosteric mechanism

AA George, SJ John, LM Lucero, JB Eaton… - The FASEB …, 2024 - ncbi.nlm.nih.gov
This study was undertaken to identify and characterize the first ligands capable of selectively
identifying nicotinic acetylcholine receptors containing α7 and β2 subunits (α7β2‐nAChR …

Insights into dynamic changes in ADC-7 and P99 cephalosporinases using small angle x-ray scattering (SAXS)

I Kumar, A Sagar, K Dhiman, CR Bethel… - Journal of …, 2024 - Taylor & Francis
To counter the emergence of β-lactamase (BL) mediated resistance, design of new β-
lactamase inhibitors (BLIs) is critical. Many high-resolution crystallographic structures of BL …