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Dashti H, Westler WM, Markley JL, et al. Unique identifiers for small molecules enable rigorous labeling of their atoms. Sci Data. 2017;4:170073doi: 10.1038/sdata.2017.73.
Dashti, H., Westler, W. M., Markley, J. L., & Eghbalnia, H. R. (2017). Unique identifiers for small molecules enable rigorous labeling of their atoms. Scientific data, 4170073. https://doi.org/10.1038/sdata.2017.73
Dashti, Hesam, et al. "Unique identifiers for small molecules enable rigorous labeling of their atoms." Scientific data vol. 4 (2017): 170073. doi: https://doi.org/10.1038/sdata.2017.73
Dashti H, Westler WM, Markley JL, Eghbalnia HR. Unique identifiers for small molecules enable rigorous labeling of their atoms. Sci Data. 2017 May 23;4:170073. doi: 10.1038/sdata.2017.73. PMID: 28534867; PMCID: PMC5441290.
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Sci Data. 2017 May 23;4:170073. doi: 10.1038/sdata.2017.73.

Unique identifiers for small molecules enable rigorous labeling of their atoms.

Scientific data

Hesam Dashti, William M Westler, John L Markley, Hamid R Eghbalnia

Affiliations

  1. National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

PMID: 28534867 PMCID: PMC5441290 DOI: 10.1038/sdata.2017.73

Abstract

Rigorous characterization of small organic molecules in terms of their structural and biological properties is vital to biomedical research. The three-dimensional structure of a molecule, its 'photo ID', is inefficient for searching and matching tasks. Instead, identifiers play a key role in accessing compound data. Unique and reproducible molecule and atom identifiers are required to ensure the correct cross-referencing of properties associated with compounds archived in databases. The best approach to this requirement is the International Chemical Identifier (InChI). However, the current implementation of InChI fails to provide a complete standard for atom nomenclature, and incorrect use of the InChI standard has resulted in the proliferation of non-unique identifiers. We propose a methodology and associated software tools, named ALATIS, that overcomes these shortcomings. ALATIS is an adaptation of InChI, which operates fully within the InChI convention to provide unique and reproducible molecule and all atom identifiers. ALATIS includes an InChI extension for unique atom labeling of symmetric molecules. ALATIS forms the basis for improving reproducibility and unifying cross-referencing across databases.

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