Alchemical free energy calculations are a useful tool for predicting free energy differences
associated with the transfer of molecules from one environment to another. The hallmark of …

Ligand binding affinity calculations based on molecular dynamics (MD) simulations and non-
physical (alchemical) thermodynamic cycles have shown great promise for structure-based …

Alchemical relative binding free energy calculations have recently found important
applications in drug optimization. A series of congeneric compounds are generated from a …

Binding free energy calculations have become increasingly valuable to drive decision
making in drug discovery projects. However, among other issues, inadequate sampling can …

Alchemical free energy perturbation (FEP) is a rigorous and powerful technique to calculate
the free energy difference between distinct chemical systems. Here we report our …

Protein–protein binding is fundamental to most biological processes. It is important to be
able to use computation to accurately estimate the change in protein–protein binding free …

Changes in protein stability due to side-chain mutations are evaluated by alchemical free-
energy calculations based on classical molecular dynamics (MD) simulations in explicit …

Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus
into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which …

Methods for calculating the relative binding free energy (RBFE) between ligands to a target
protein are gaining importance in the structure-based drug discovery domain, especially as …

自然界亿万年的进化孕育出了丰富的天然产物资源, 进而为药物研发提供了巨大的分子宝库.
进化导向生物信息学方法在微生物天然产物研究中发挥着越来越重要的作用 …