We computed relative binding free energies using GPU accelerated Thermodynamic
Integration (GPU-TI) on a dataset originally assembled by Schrödinger, Inc.. Using their GPU …

With renewed interest in free energy methods in contemporary structure-based drug design,
there is a pressing need to validate against multiple targets and force fields to assess the …

Alchemical free energy methods, such as free energy perturbation (FEP) and
thermodynamic integration (TI), become increasingly popular and crucial for drug design …

Biomolecular simulations have become an essential tool in contemporary drug discovery,
and molecular mechanics force fields (FFs) constitute its cornerstone. Developing a high …

Alchemical free energy (AFE) calculations based on molecular dynamics (MD) simulations
are key tools in both improving our understanding of a wide variety of biological processes …

Accurate absolute binding free-energy estimation in silico, following either an alchemical or
a geometrical route, involves several subprocesses and requires the introduction of …

Tuesday, February 13, 2024 423a the stability change by the mutation. These predictions
give us clues to improve the target without synthesizing/expressing the target. However …

Absolute binding free energy (ABFE) calculations with all-atom molecular dynamics (MD)
have the potential to greatly reduce costs in the first stages of drug discovery. Here we …

Designing ligands that bind their target biomolecules with high affinity and specificity is a key
step in small-molecule drug discovery, but accurately predicting protein–ligand binding free …

Relative binding free energy (RBFE) calculations are widely used to aid the process of drug
discovery. TIES, Thermodynamic Integration with Enhanced Sampling, is a dual-topology …