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Composite Graph Neural Networks for Molecular Property Prediction [PDF]

International Journal of Molecular Sciences
Graph Neural Networks have proven to be very valuable models for the solution of a wide variety of problems on molecular graphs, as well as in many other research fields involving graph-structured data.
Pietro Bongini, Marco Maggini, Mónica Bianchini   +2 more
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On the centrality of vertices of molecular graphs

Journal of Computational Chemistry, 2013
For acyclic systems the center of a graph has been known to be either a single vertex of two adjacent vertices, that is, an edge. It has not been quite clear how to extend the concept of graph center to polycyclic systems. Several approaches to the graph center of molecular graphs of polycyclic graphs have been proposed in the literature. In most cases
Milan Randic, Marjana Novic, Marjan Vracko, Dejan Plavsic   +3 more
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On the Complexity of Molecular Graphs

MATCH : communications in mathematical and in computer chemistry, 1999
On the Complexity of Molecular ...
Nikolić, Sonja, Trinajstić, Nenad, Tolić, Iva Marija   +2 more
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Graph Databases in Molecular Biology

2018
In recent years, the increase in the amount of data generated in basic social practices and specifically in all fields of research has boosted the rise of new database models, many of which have been employed in the field of Molecular Biology. NoSQL graph databases have been used in many types of research with biological data, especially in cases where
Waldeyr Mendes Cordeiro da Silva, Polyane Wercelens, Maria Emília M. T. Walter, Maristela Holanda, Marcelo M. Brigido   +4 more
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Topological Indices Based on the Line Graph of the Molecular Graph

Journal of Chemical Information and Computer Sciences, 1996
The topological index e recently proposed by one of the authors [E. Estrada, J. Chem. Inf. Comput. Sci. 1995, 35, 31−33] is shown to be identical to the connectivity index of the line graph of the molecular graph. This observation makes it possible to conceive a whole class of novel, line-graph-based topological indices.
Ivan Gutman, Ernesto Estrada
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Graph-Based Molecular Alignment (GMA)

Journal of Chemical Information and Modeling, 2007
We describe a combined 2D/3D approach for the superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency: the suggested approach ...
Jörn Marialke, Robert Körner, Simon Tietze, Joannis Apostolakis   +3 more
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Graphs in Molecular Epidemiology

2021
AbstractGraphs and networks are used in molecular epidemiology to model the evolution of viruses and their spread during outbreaks and epidemics. They are instrumental at different stages of the computational pipelines. This includes the inference of transmission networks using viral sequences sampled from infected individuals, and studies of selection
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Graph Valence Shells as Molecular Descriptors

Journal of Chemical Information and Computer Sciences, 2001
We have introduced a new simple structural descriptor for molecules that is based on the count of the valence shells for vertices in molecular graphs. The construction of the new descriptor is illustrated on 2,3-dimethylhexane and is reported for the 18 octane isomers.
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Graph Data Management for Molecular Biology

OMICS: A Journal of Integrative Biology, 2003
IT IS OUR VIEW that labeled directed graph data models (simple, nested, or hypergraphs) can naturally and usefully capture a wide variety of biological data and queries. We believe that development of general purpose graph data management systems (GDMSs) could become major platforms for development of a wide variety of bioinformatics database systems ...
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Novel Shape Descriptors for Molecular Graphs

Journal of Chemical Information and Computer Sciences, 2001
We report on novel graph theoretical indices which are sensitive to the shapes of molecular graphs. In contrast to the Kier's kappa shape indices which were based on a comparison of a molecular graph with graphs representing the extreme shapes, the linear graph and the "star" graph, the new shape indices are obtained by considering for all atoms the ...
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