Computing cyclic invariants for molecular graphs

Berger, Franziska; Gritzmann, Peter; Vries, Sven de

doi:10.1002/net.21757

Cited by 4 publications

(6 citation statements)

References 33 publications

(68 reference statements)

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“…Cycles in molecular graphs have been shown to be good representations of the structure of molecular systems. ,, We herein propose a representation of each conformer identified over a trajectory based on a well-chosen set of cycles of its 2D-MolGraph, mainly the ones containing at least one H-Bond, in order to be able to quantify and follow in time the changes in the H-Bonded network of the molecular structures. The conformational changes that are targeted herein are solely induced by the dynamics of the H-Bonded network.…”

Section: Methodsmentioning

confidence: 99%

“…Previous work has shown the relevance of modeling the structure of a molecular system by the interaction of the cycles of the associated molecular graph, i.e., their intersection in terms of vertices and links. ,− Such a representation of a molecule by the interactions of a representative subset of cycles has also been seen as an extension of the reduction of the Markush structure of a molecule into a cyclic/noncyclic reduction scheme. In particular, this made it possible to express the central structure of a molecule for classification purposes. , Sets of molecules have thus been classified and characterized, , and open-service libraries providing specific cycles in graph molecules are available. , …”

Section: Introductionmentioning

confidence: 99%

“…In particular, this made it possible to express the central structure of a molecule for classification purposes. 21,22 Sets of molecules have thus been classified and characterized, 19,23 and open-service libraries providing specific cycles in graph molecules are available. 20,21 Such a representation by the interaction of particular cycles is given by considering graphs of cycles, 24 i.e., graphs in which vertices are these cycles and edges represent the interactions between these cycles.…”

Section: Introductionmentioning

confidence: 99%

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Time-Resolved Graphs of Polymorphic Cycles for H-Bonded Network Identification in Flexible Biomolecules

Aboulfath,

Bougueroua,

Cimas

et al. 2024

J. Chem. Theory Comput.

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A novel approach based on a coarse-grained representation of topological graphs is proposed for the automatic analysis of molecular dynamics (MD) trajectories of hydrogenbonded (H-Bonded) flexible biomolecules. Herein, our approach models an H-Bonded biomolecule by its H-Bonded cycles and its graph of cycles in which the vertices and links represent the intersections between these cycles. We propose a methodology in which each identified conformer/isomer from the MD is represented by a well-chosen set of H-Bonded cycles called a minimum cycle basis. The key component is the "polycycles" that distinguish the cycles that play the same polymorphic role in the molecule from the ones that lead to an actual conformational change of the molecule. The relevance of our proposed method is evaluated on MD trajectories of gas-phase biomolecules, for which the covalent bonds are unchanged over time and only the hydrogen bonds change over time. The polygraphs and their time evolution are shown to reveal the dynamicity of the metastructure(s) of the H-Bonded biomolecules while providing polymorphic information on the cycles. Such information on the dynamics and changes in the H-bond network, as some cycles change identity while retaining the same role in the overall structure, is not easily captured at the atomic level of representation. Such information can instead be captured by polymorphic cycles.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Time-Resolved Graphs of Polymorphic Cycles for H-Bonded Network Identification in Flexible Biomolecules

Aboulfath,

Bougueroua,

Cimas

et al. 2024

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

“…With the rapid progress of electronic devices and communication technologies, it promotes the advent of the era of cloud computing that has an important impact and value on all walks of life [1,2]. Cloud computing also speeds up data outsourcing service and makes it an important and convenient application [3,4].…”

Section: Introductionmentioning

confidence: 99%

Privacy‐Guarding Optimal Route Finding with Support for Semantic Search on Encrypted Graph in Cloud Computing Scenario

Chen

et al. 2021

Wireless Communications and Mobile Computing

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The arrival of cloud computing age makes data outsourcing an important and convenient application. More and more individuals and organizations outsource large amounts of graph data to the cloud computing platform (CCP) for the sake of saving cost. As the server on CCP is not completely honest and trustworthy, the outsourcing graph data are usually encrypted before they are sent to CCP. The optimal route finding on graph data is a popular operation which is frequently used in many fields. The optimal route finding with support for semantic search has stronger query capabilities, and a consumer can use similar words of graph vertices as query terms to implement optimal route finding. Due to encrypting the outsourcing graph data before they are sent to CCP, it is not easy for data customers to manipulate and further use the encrypted graph data. In this paper, we present a solution to execute privacy-guarding optimal route finding with support for semantic search on the encrypted graph in the cloud computing scenario (PORF). We designed a scheme by building secure query index to implement optimal route finding with support for semantic search based on searchable encryption idea and stemmer mechanism. We give formal security analysis for our scheme. We also analyze the efficiency of our scheme through the experimental evaluation.

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“…With the blossom of cloud computing [1], [2], data outsourcing has become a popular trend. The application for a graph is pretty common, such as social network graph [3], collaboration network [4], and molecular graph [5]. Considering the benefits of data outsourcing in cloud computing, lots of graph data are outsourced to the cloud.…”

Section: Introductionmentioning

confidence: 99%

Secure and Efficient Adjacency Search Supporting Synonym Query on Encrypted Graph in the Cloud

Zhao

Cui

et al. 2019

IEEE Access

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With the popularity of cloud computing, cloud outsourcing has aroused great concern in academia. A lot of graph data are outsourced to the cloud for saving cost. As the cloud server may be not entirely reliable, the outsourced graph data are usually encrypted before sending to the cloud for the security considerations. Adjacency search is a basic operation, and many other operations can be performed based on the adjacency search. Adjacency search supporting synonym query is a more meaningful operation which can make a query user improve the scope of the query. Due to the graph data being encrypted in the cloud, adjacency search supporting synonym query becomes a very challenging task. In this paper, we propose an efficient solution to perform privacy-assured adjacency search supporting synonym query on the encrypted graph in the cloud (PASQ). Our work utilizes a stemming algorithm and an encryption mechanism to perform adjacency search. A query user can get a wider range of search results by this solution, and the privacy of query will not be disclosed. We present a design scheme for the outsourced graph and analyze the security. We demonstrate the efficiency of our scheme by the experiment results on a real graph data.

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Computing cyclic invariants for molecular graphs

Cited by 4 publications

References 33 publications

Time-Resolved Graphs of Polymorphic Cycles for H-Bonded Network Identification in Flexible Biomolecules

Time-Resolved Graphs of Polymorphic Cycles for H-Bonded Network Identification in Flexible Biomolecules

Privacy‐Guarding Optimal Route Finding with Support for Semantic Search on Encrypted Graph in Cloud Computing Scenario

Secure and Efficient Adjacency Search Supporting Synonym Query on Encrypted Graph in the Cloud

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