Abstract: Embodiments of the invention include systems and methods that enable the identification of candidate proteins that have desired features of a target protein. An example method comprises receiving first and second input proteins. The method further comprises applying a first machine learning model to the first and second input proteins to generate corresponding fragments. The method further comprises applying a second machine learning model to the fragments, wherein applying the second machine learning model comprises generating an encoded representation in a multidimensional space for each of the fragments. The method also comprises generating a similarity score between the fragments from the first input and the second input. The method then comprises generating a hierarchical scale of similarity between the first and second inputs according to the similarity score and selecting candidate proteins based on the hierarchical scale.