3 papers
physics.chem-ph2026
Solv-eze: Automated Placement of Explicit Water Molecules Using 3D-RISM
Felipe Silva Carvalho, Steven Ramsey, Tom Kurtzman +2
Molecular dynamics (MD) simulations are widely used to study biological systems, where water molecules often play a critical role in protein-ligand interactions. In conventional MD…
physics.chem-ph2026
Development of an Optimized Parameter Set for Monovalent Ions in the Reference Interaction Site Model of Solvation
Felipe Silva Carvalho, Alexander McMahon, David A. Case +1
Accurate modeling of aqueous monovalent ions is essential for understanding the function of biomolecules, such as nucleic acid stability and binding of charged drugs to protein tar…
physics.chem-ph2025
Automated Workflow for Absolute Binding Free Energy Calculations with Implicit Solvent and Double Decoupling
Steven Ayoub, Michael Barton, David A. Case +1
Accurate absolute binding free energy (ABFE) calculations can reduce the time and cost of identifying drug candidates from a diverse pool of molecules that may have been overlooked…