Reply to "Letter to the editor: methodological considerations in the benchmarking of AI-based protein-aptamer complex prediction".

Abstract

We thank MD Kazim Okan Dolu for their interest in our published work and for the opportunity to clarify several points regarding software versioning, benchmark independence, secondary-structure generation, binding-free-energy terminology, and negative-control design. We acknowledge that several descriptions in the original manuscript could be stated more precisely. These clarifications improve the transparency and reproducibility of the study, but do not affect the reported analyses or main conclusions.