Valery Tkachenko

Publications of Valery Tkachenko

• Towards a gold standard: regarding quality in public domain chemistry databases and approaches to improving the situation.

  Authors: Antony J Williams, Sean Ekins, Valery Tkachenko

  Drug discovery today. 03/2012;

  In recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used forIn recent years there has been a dramatic increase in the number of freely accessible online databases serving the chemistry community. The internet provides chemistry data that can be used for data-mining, for computer models, and integration into systems to aid drug discovery. There is however a responsibility to ensure that the data are high quality to ensure that time is not wasted in erroneous searches, that models are underpinned by accurate data and that improved discoverability of online resources is not marred by incorrect data. In this article we provide an overview of some of the experiences of the authors using online chemical compound databases, critique the approaches taken to assemble data and we suggest approaches to deliver definitive reference data sources.

• Identification of "known unknowns" utilizing accurate mass data and ChemSpider.

  Authors: James L Little, Antony J Williams, Alexey Pshenichnov, Valery Tkachenko

  Journal of the American Society for Mass Spectrometry. 11/2011; 23(1):179-85.

  In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns."In many cases, an unknown to an investigator is actually known in the chemical literature, a reference database, or an internet resource. We refer to these types of compounds as "known unknowns." ChemSpider is a very valuable internet database of known compounds useful in the identification of these types of compounds in commercial, environmental, forensic, and natural product samples. The database contains over 26 million entries from hundreds of data sources and is provided as a free resource to the community. Accurate mass mass spectrometry data is used to query the database by either elemental composition or a monoisotopic mass. Searching by elemental composition is the preferred approach. However, it is often difficult to determine a unique elemental composition for compounds with molecular weights greater than 600 Da. In these cases, searching by the monoisotopic mass is advantageous. In either case, the search results are refined by sorting the number of references associated with each compound in descending order. This raises the most useful candidates to the top of the list for further evaluation. These approaches were shown to be successful in identifying "known unknowns" noted in our laboratory and for compounds of interest to others.

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• Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining.

  Authors: Kristina M Hettne, Antony J Williams, Erik M van Mulligen, Jos Kleinjans, Valery Tkachenko, Jan A Kors

  Journal of cheminformatics. 01/2010; 2(1):4.

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