It is important to also note that a priori system specific knowledge remains crucial in ensuring the performance of alchemical methods. Whilst one of the main advantages of ABFE calculations being of directly estimating the affinity of a binder, having access to experimental affinities for a subset of the calculated binders to the same target or a structurally similar one, would significantly help in identifying and adjusting issues in a model. For example, we were able to confidently use an N-terminal truncated model of the PWWP1 system (see SI Text 2)