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. 2020 Jul 3;7:210. doi: 10.1038/s41597-020-0547-y

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© The Author(s) 2020

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — Workflow of the web server. For a given small molecule, the web server queries ALATIS to retrieve unique atom labels of the compound. The preprocessing module converts the structure file to a graph data structure, and extracts chain and ring molecular fragments. Then every fragment is analyzed to identify saccharide fingerprints. If no fingerprint found, the fragment is used in calculating a compound penalty. The molecular fragments that contain saccharide fingerprints are used in calculating the minimum fragment penalty. This penalty and the compound penalty are then used in calculating the probabilities. The web server reports the calculated probabilities and also lists every other calculated fragment penalty for the molecular fragments. In parallel, the web server uses the Open Babel package for identifying ligands with the highest structural similarities to the submitted molecule. These ligands from the RCSB PDB Ligand Expo are cross-referenced to the PDB molecular complexes. The outcome of this structural analysis reports proteins from PDB that bind to the identified ligands.