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

Cited by (120)

Items 101–120 of 120

1. PySteMoDA: An Open-Source Python Package for the Analysis of Steered Molecular Dynamics Simulations Data
   Ismahene Mesbah, Colin Klaus, Marcos Sotomayor, Fidan Sumbul, Félix Rico · 2026 · bioRxiv
2. Structure-Guided Discovery of Potent Polo-Like Kinase 1 Inhibitors for Breast Cancer Therapy
   Michael Afiadenyo, Sherif Hamidu, D. Obiri-Yeboah, S. K. Amponsah, Kwabena Dankwah, Latif Adams · 2026 · Journal of Pharmaceutical Innovation
3. Investigation on the Molecular Mechanism of ORF7a Suppressing BST-2 Antiviral Activity through Structural Modeling of Their Protein-Protein Interface.
   Min-Kang Hsieh, Jeffery B. Klauda · 2026 · Journal of Physical Chemistry B
4. Full Reaction Pathway Dynamics for Atmospheric Decomposition Reactions: The Photodissociation of H$_2$COO
   Cang-Tao Yin, Markus Meuwly · 2026
5. Molecular Insights Into the Ionic Assembly of Poly‐Galacturonic Acid Oligomers—Impact of Charge, Ionic Radius, and Polymer Functionalization
   L. Bu, Michael F. Crowley, Deepak Sharma, B. Urbanowicz, Vivek S. Bharadwaj · 2025 · Journal of Computational Chemistry
6. Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design
   H. Michel, Anne M. Brown, Alexander D. MacKerell, Justin A. Lemkul · 2025 · bioRxiv
7. MDCompress: better, faster compression of molecular dynamics simulation trajectories
   2026
8. Synergistic Computational Approaches for Accelerated Drug Discovery: Integrating Quantum Mechanics, Statistical Thermodynamics, and Quantum Computing
   Farzad Molani, Art E. Cho · 2025
9. MDcraft - A modern molecular dynamics simulation package with machine learning potentials support
   I. S. Galtsov, R. Muratov, G. V. Vyskvarko, S. Murzov, S. Dyachkov, P. Levashov · 2025 · Computer Physics Communications
10. Structure and Spectroscopy of Criegee Intermediates in Gas‐ and Aqueous Environments
    Cang-Tao Yin, Meenu Upadhyay, Markus Meuwly · 2025 · Helvetica Chimica Acta
11. Tripeptide dynamics from empirical and machine-learned energy functions
    S. Aydın, Valerii Andreichev, Pantelis Maragkoudakis, Markus Meuwly · 2025 · Biophysical Journal
12. Charge Neutralization During Peptide Transport in the Bacterial SecYEG Translocon
    Laura Nübl, Собакинская Екатерина Александровна, Frank Müh · 2025 · Biomolecules
13. Molecular Simulations of Ladderane Lipid Bilayers as Initial Models for Anammox Bacteria.
    Vincent Zhao, Jeffery B. Klauda · 2025 · Journal of Physical Chemistry B
14. GridFF: Efficient Simulation of Organic Molecules on Rigid Substrates
    I. Mal, Milan Kočí, P. Nicolini, P. Hapala · 2025 · Journal of Chemical Theory and Computation
15. End-to-End Photodissociation Dynamics of Energized H$_2$COO
    Cang-Tao Yin, Silvan Kaser, Meenu Upadhyay, Markus Meuwly · 2025
16. From sequence to protein structure and conformational dynamics with AI/ML
    Alexander M. Ille, Emily Anas, Michael B. Mathews, Stephen K. Burley · 2025
17. Quantum Coulombic Interactions Mediate Free Radical Control in Radical SAM Viperin/RSAD2.
    M. Khalilian, G. DiLabio · 2025 · Journal of the American Chemical Society
18. PME Switching in Confinement Simulations of Charged Solutes.
    A. van der Vaart, Sang T. Le Phan · 2024 · Journal of Physical Chemistry A
19. Diffusion and Spectroscopy of H2 in Myoglobin
    Jiri Käser, Kai Töpfer, Markus Meuwly · 2024 · Oxygen
20. Multi-Criteria Optimisation: The Environment-Dependent Protein Folding Process Simulation Tool
    I. Roterman, Katarzyna Stąpor, D. Dułak, L. Konieczny · 2026 · Advances in Pure Mathematics