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During the last few years, the main reason for using molecular structure databases has changed.
Here, searching in spectral libraries is replaced by searching in molecular structure databases.
Different from the above, some authors propose to use molecular structure databases to determine the candidate molecular formulas [112].
With recent methodical advances in the field [9 15], MS/MS data is increasingly searched in molecular structure databases.
Second, although hyperparameters of the priors are determined from molecular structure databases, we do not train our method using these databases.
With the advent of novel computational approaches [169, 206, 207], searching spectral libraries may be replaced by searching molecular structure databases within in the next five to ten years.
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Three-dimensional reconstructions of mature 40S and pre-40S ribosomal subunits have been deposited in the EMBL-EBI Molecular Structure Database (http://www.ebi.ac.uk/msd/) and can be retrieved under accession numbers EMD-1211 and EMD-1212.
PubChem [11] is the largest publicly available molecular structure database.
The predicted fingerprints are used to search a molecular structure database for metabolite identification.
In this way, a rule-based fragmenter can be used to search in a molecular structure database.
Rather, we assume that the prior assumptions will hold for any biomolecule, and use the molecular structure database solely to estimate the hyperparameters.
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