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StructRecon is a cheminformatics tool for automatically determining the structure of compounds from given database identifiers.

StructRecon traverses the cross-references between chemical databases in order to obtain a more complete view of the information available on any given compound. This allows StructRecon to resolve structures for database identifiers which may not directly contain the structure. In the case where the program finds multiple conflicting chemical structures, a random-walk based scoring algorithm is used to determine the most likely structure.

StructRecon is written in Python, and the source code is available at GitHub. It accompanies the paper

  • Reconciling Inconsistent Molecular Structures from Biochemical Databases
    Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg, Daniel Merkle
    Accepted at ISBRA 2023 [ TR ]

If you choose to use StructRecon in your research, we kindly ask you to cite this paper.

Interactive interface

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Below are some examples for identifier graphs generated by StructRecon, each showing the database links from a single database identifier:

Water (BiGG: M_h2o) Water

5-Methylthio-D-ribose (BiGG: M_5mtr) 5MTR