Petri nets formalism facilitates analysis of complex biomolecular structural data

DOI10.1051/RO/2015043MaRDI QIDQ2805502zbMATH OpenOpenAlexWikidataFDO

Authors Anna Gogolinska, Rafal Jakubowski, Wieslaw Nowak

Publication date 11 May 2016

Published in RAIRO. Operations Research (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1051/ro/2015043

zbMATH Keywords

clusteringconformational spacedata mininggraphsmolecular dynamic simulationsPetri net

Mathematics Subject Classification ID

Algorithms in computer science (68W99) Deterministic network models in operations research (90B10) Computational methods for problems pertaining to biology (92-08)

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Cites work

• scientific article; zbMATH DE number 3885321 (Why is no real title available?)
• scientific article; zbMATH DE number 3557247 (Why is no real title available?)
• Principal component analysis.

Cited in

(2)

• Recent advances in operations research in computational biology, bioinformatics and medicine
• A survey of algorithms for transforming molecular dynamics data into metadata for \textit{in situ} analytics based on machine learning methods

Describes a project that uses

Uses Software

• NAMD
• VMD
• BioJava
• CHARMM
• Gromacs

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