Dataset Information

FlavorDB: a database of flavor molecules.

ABSTRACT: Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives. Given their utility in various spheres of life such as food and fragrances, it is valuable to have a repository of flavor molecules, their natural sources, physicochemical properties, and sensory responses. FlavorDB (http://cosylab.iiitd.edu.in/flavordb) comprises of 25,595 flavor molecules representing an array of tastes and odors. Among these 2254 molecules are associated with 936 natural ingredients belonging to 34 categories. The dynamic, user-friendly interface of the resource facilitates exploration of flavor molecules for divergent applications: finding molecules matching a desired flavor or structure; exploring molecules of an ingredient; discovering novel food pairings; finding the molecular essence of food ingredients; associating chemical features with a flavor and more. Data-driven studies based on FlavorDB can pave the way for an improved understanding of flavor mechanisms.

SUBMITTER: Garg N

PROVIDER: S-EPMC5753196 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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FlavorDB: a database of flavor molecules.

Garg Neelansh N Sethupathy Apuroop A Tuwani Rudraksh R Nk Rakhi R Dokania Shubham S Iyer Arvind A Gupta Ayushi A Agrawal Shubhra S Singh Navjot N Shukla Shubham S Kathuria Kriti K Badhwar Rahul R Kanji Rakesh R Jain Anupam A Kaur Avneet A Nagpal Rashmi R Bagler Ganesh G

Nucleic acids research 20180101 D1

Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives. Given their utility in various spheres of life such as food and fragrances, ...[more]

PMID: 29059383

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Project description:BACKGROUND:Interactions between ions and proteins have been extensively studied, yet most of the studies focus on the ion binding site. The binding mechanism for many ion binding sites can be clearly described from high resolution structures. Although knowledge accumulated on a case-by-case basis is valuable, it is also important to study the ion-protein interaction statistically. From experimentally determined structures, it is possible to examine the ion distribution around each amino acid. Such distributions can reveal relation between ions and amino acids, so it is desirable to carry out a systematic survey of 'ion-amino acid' pairing interaction and share the information with a publicly available database. RESULTS:The survey in the Protein Data Bank (PDB) revealed that approximately 40% of molecules records contain at least one ion. To reduce the bias resulted from protein redundancy, the statistics were extracted from a non-redundant dataset by excluding the proteins with similar sequences. Based on the structures of protein molecules and the location of ions, the statistical distributions of ions around each proteinogenic amino acid type were investigated and further summarized in a database. To systematically quantify the interactions between ions and each amino acid, the positions of ions were mapped to the coordinate system centered at each neighboring amino acid. It was found that the distribution of ions follows the expected rules governed by the physicochemical interactions in general. Large variations were observed, reflecting the preference in 'ion-amino acid' interactions. The analysis program is written in the Python programming language. The statistical results and program are available from the online database: ion distribution in protein molecules (IDPM) at http://liulab.csrc.ac.cn/idpm/ . CONCLUSION:The spatial distribution of ions around amino acids is documented and analyzed. The statistics can be useful for identifying ion types for a given site in biomolecules, and can be potentially used in ion position prediction for given structures.

Dataset Information

FlavorDB: a database of flavor molecules.

Publications

FlavorDB: a database of flavor molecules.

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