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In this paper, we present a novel approach called \u201cMolecular Anatomy\u201d as a flexible and unbiased molecular scaffold-based metrics to cluster large set of compounds. We introduce a set of nine molecular representations at different abstraction levels, combined with fragmentation rules, to define a multi-dimensional network of hierarchically interconnected molecular frameworks. We demonstrate that the introduction of a flexible scaffold definition and multiple pruning rules is an effective method to identify relevant chemical moieties. This approach allows to cluster together active molecules belonging to different molecular classes, capturing most of the structure activity information, in particular when libraries containing a huge number of singletons are analyzed. We also propose a procedure to derive a network visualization that allows a full graphical representation of compounds dataset, permitting an efficient navigation in the scaffold\u2019s space and significantly contributing to perform high quality SAR analysis. The protocol is freely available as a web interface at\n                    <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/ma.exscalate.eu\">https:\/\/ma.exscalate.eu<\/jats:ext-link>\n                    .\n                  <\/jats:p>","DOI":"10.1186\/s13321-021-00526-y","type":"journal-article","created":{"date-parts":[[2021,7,23]],"date-time":"2021-07-23T06:03:07Z","timestamp":1627020187000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":21,"title":["\u201cMolecular Anatomy\u201d: a new multi-dimensional hierarchical scaffold analysis tool"],"prefix":"10.1186","volume":"13","author":[{"given":"Candida","family":"Manelfi","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marica","family":"Gemei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carmine","family":"Talarico","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carmen","family":"Cerchia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anna","family":"Fava","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Filippo","family":"Lunghini","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6830-2695","authenticated-orcid":false,"given":"Andrea Rosario","family":"Beccari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,7,23]]},"reference":[{"key":"526_CR1","doi-asserted-by":"publisher","first-page":"904","DOI":"10.1038\/nchembio.1937","volume":"11","author":"R Macarron","year":"2015","unstructured":"Macarron R (2015) Chemical libraries: how dark is HTS dark matter? 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