MOTIVATION: Protein structure comparison is pivotal for deriving homological relationships, elucidating protein functions, and understanding evolutionary developments. The burgeoning field of in-silico protein structure prediction now yields billions of models with near-experimental accuracy, necessitating sophisticated tools for discerning structural similarities among proteins, particularly when sequence similarity is limited. RESULTS: In this article, we have developed the align distance matrix with scale (ADAMS) pipeline, which synergizes the distance matrix alignment method with the scale-invariant feature transform algorithm, streamlining protein structure comparison on a proteomic scale. Utilizing a computer vision-centric strategy for contrasting disparate distance matrices, ADAMS adeptly alleviates challenges associated with proteins characterized by a high degree of structural flexibility. Our findings indicate that ADAMS achieves a level of performance and accuracy on par with Foldseek, while maintaining similar speed. Crucially, ADAMS overcomes certain limitations of Foldseek in handling structurally flexible proteins, establishing it as an efficacious tool for in-depth protein structure analysis with heightened accuracy. AVAILABILITY: ADAMS can be download and used as a python package from Python Package Index (PyPI): adams · PyPI. Source code and other materials are available from young55775/ADAMS-developing (github.com). An online server is available: Bseek Search Server (cryonet.ai).