Graph Databases in Molecular Biology

Silva, Waldeyr Mendes Cordeiro da; Wercelens, Polyane; Walter, Maria Emília M. T.; Holanda, Maristela; Brigido, Marcelo M.

doi:10.1007/978-3-030-01722-4_5

Cited by 12 publications

(9 citation statements)

References 36 publications

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“…Yet, they do not scale up to the recent increase of data and species available. Graph-databases [ 95 ] and GraphQL APIs are promising tools for this task, for their ability to accommodate and connect more heterogeneous data. Efforts within the structural bioinformatics community to adopt these technologies and increase connectivity are also notable [ 96 ] but are still far from being the go-to model.…”

Section: Computational Challenges For Quantifying Heterogeneity Frmentioning

confidence: 99%

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

Poitevin

Kushner

et al. 2020

Molecules

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The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal motion at the single particle level, specialization at the cellular and subcellular scale, or evolutionary differences across species. Upon solving the ribosome atomic structure at medium to high resolution, cryogenic electron microscopy (cryo-EM) has enabled investigating all these forms of heterogeneity. In this review, we present some recent advances in quantifying ribosome heterogeneity, with a focus on the conformational and evolutionary variations of the ribosome and their functional implications. These efforts highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data, which would more generally benefit the study of molecular dynamics and evolution of proteins and other complexes.

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Section: Computational Challenges For Quantifying Heterogeneity Frmentioning

confidence: 99%

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

Poitevin

Kushner

et al. 2020

Molecules

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“…Another matter is how to express them properly. Graph databases are a suitable tool for this purpose that has been demonstrated to be an efficient and convenient way to store and explore metabolic networks [36,37]. Here, we used a proposed graph database (2Path-Sesquiterpenes) to store and enrich the simulation data with experimental evidence related to the predicted sesquiterpenes, the Scenarios.…”

Section: Path-sesquiterpenes Databasementioning

confidence: 99%

“…NoSQL Graph Databases are Database Management Systems (DBMS) that can store graphs natively. They have been used in research with biological data, especially in cases where data integration is a determining factor [37]. In this work, we have used the Neo4J graph database to optionally store both the generated sesquiterpenes biosynthesis pathways and the previous data knowledge from Scenarios.…”

Section: Database Storagementioning

confidence: 99%

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

et al. 2019

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Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases that admit different cyclizations and rearrangements to yield a blend of sesquiterpenes. Here, we investigate to what extent sesquiterpene biosynthesis metabolic pathways can be reconstructed just from the knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and to elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β -caryophyllene, α -humulene, and β -farnesene. We also introduce a graph database to integrate the simulation results with experimental biological evidence for the selected predicted sesquiterpenes biosynthesis.

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“…Thus they are a potentially valuable resource, which can be leveraged more efficiently if the data are provided with a comprehensive and consistent data schema can support the FAIR Guiding Principles for scientific data management [37] and facilitate the exchange and interoperability. Graph databases are a suitable tool for this purpose that has been demonstrated to be an efficient and convenient way to store and explore metabolic networks [38,39]. Here we use a graph database to enriches simulation data with experimental evidence related to the predicted sesquiterpenes.…”

Section: Database Storagementioning

confidence: 99%

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

Silva¹,

Andersen

Holanda³

et al. 2019

Preprint

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Plants produce a diverse portfolio of sesquiterpenes that are important in their response to herbivores and the interaction with other plants. Their biosynthesis from farnesyl diphosphate depends on the sesquiterpene synthases. Here, we investigate to what extent metabolic pathways can be reconstructed just from knowledge of the final product and the reaction mechanisms catalyzed by sesquiterpene synthases. We use the software package MedØlDatschgerl (MØD) to generate chemical networks and elucidate pathways contained in them. As examples, we successfully consider the reachability of the important plant sesquiterpenes β-caryophyllene, α-humulene, and β-farnesene. We also introduce a graph database to integrate simulation results with experimental biological evidence for selected predicted sesquiterpenes biosynthesis.

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Graph Databases in Molecular Biology

Cited by 12 publications

References 36 publications

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

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