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UID:submissions.pasc-conference.org_PASC24_sess165_msa309@linklings.com
SUMMARY:GPU-Accelerated Molecular Dynamics Simulations for Multistate Bind
 ing Affinity Calculations with RE-EDS
DESCRIPTION:Minisymposium\n\nEnrico Ruijsenaars (ETH Zurich)\n\nComputatio
 nal approaches for estimating protein-ligand binding affinities are crucia
 l in modern drug discovery. All-atom explicit-solvent molecular dynamics (
 MD) simulations use the foundational principles of classical mechanics and
  statistical thermodynamics to rigorously calculate binding free energies.
  They are the most accurate affinity prediction methods that are still tra
 ctable when applied to biological systems, but they are also among the mos
 t computationally demanding. To mitigate costs, efficient sampling protoco
 ls such as multistate methods have been developed, enabling calculations o
 f relative binding free energy across multiple ligands from a single simul
 ation. One such technique, replica-exchange EDS (RE-EDS), leverages simila
 rities in ligand environments to achieve improved sampling performance com
 pared to pairwise methods. Its recent GPU-accelerated implementation in th
 e OpenMM toolkit for molecular simulation has been benchmarked on a set of
  solvation free energies from the FreeSolv dataset and forms the basis of 
 a high throughput framework for free energy calculations.\n\nDomain: Chemi
 stry and Materials, Life Sciences\n\nSession Chair: Andreas Vitalis (Unive
 rsity of Zurich)
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