Molecular Similarity: Theory, Applications, and Perspectives

24 November 2023, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


Molecular similarity pervades much of our understanding and rationalization of chemistry. This has become particularly evident in the current data-intensive era of chemical research, with similarity measures serving as the backbone of many Machine Learning (ML) supervised and unsupervised procedures. Here, we present a discussion on the role of molecular similarity in drug design, chemical space exploration, chemical “art” generation, molecular representations, and many more. We also discuss more recent topics in molecular similarity, like the ability to efficiently compare large molecular libraries.


drug design
protein dynamics
chemical space


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