(25,26) Such incorrect conclusions further undermine the field of molecular dynamics and its ability to produce reliable predictions. This is in contrast to single trajectory approaches, which are frequently not representational, leading to false positives. The different starting velocities in each replica enhance sampling and therefore improve reproducibility. (22−24) TIES uses an ensemble of MD simulations at every λ window in order to control uncertainty in molecular dynamics simulations. (20) TIES uses a modified dual-topology approach to alchemical transformations and has been shown previously to perform well in the ranking of compounds (21) and the prediction of relative binding free energies (20) with or without replica-exchange solute tempering (REST2). Here, we focus on our protocol named TIES (Thermodynamic Integration with Enhanced Sampling) for the calculation of RBFEs. TIES 20, in conjunction with the enablement of ring morphing, reduces the size of the alchemical region and significantly improves the precision of the predicted free energies.

This improvement is partly due to AM1-BCC affecting only the charges of the atoms local to the mutation, which translates to even fewer morphed atoms, consequently reducing issues with sampling and therefore ensemble averaging. We further compare the results with the AM1-BCC charge system and show that it improves agreement with the experimental data by slightly over 10%. However, the non-normal nature of the relative free energy distributions underscores the importance of ensemble simulation.

We find that increasing the ensemble size from 5 to 20 replicas per λ window only has a minimal impact on the accuracy.

Enabling the morphing of partial rings decreases the size of the alchemical region in the dual-topology transformations resulting in a significant improvement in the prediction precision. We find that TIES 20 with the RESP charge system, using the new superimposition algorithm, reproduces the previous results with mean unsigned error of 0.75 kcal/mol with respect to the experimental data. The algorithm is employed to enable matching and morphing of partial rings in the TIES protocol along with a validation study using 55 transformations and five different proteins from our previous work. We implement a flexible topology superimposition algorithm which uses an exhaustive joint-traversal for computing the largest common component(s). The validity of TIES relies on the correctness of matching atoms across compared pairs of ligands, laying the foundation for the transformation along an alchemical pathway.

The TIES (Thermodynamic Integration with Enhanced Sampling) protocol is a formally exact alchemical approach in computational chemistry to the calculation of relative binding free energies.

Super imposition