Novel topological descriptors for analyzing biological networks

Dehmer, Matthias M.; Barbarini, Nicola N.; Varmuza, Kurt K.; Graber, Armin A.
January 2010
BMC Structural Biology;2010, Vol. 10, p18
Academic Journal
Background: Topological descriptors, other graph measures, and in a broader sense, graph-theoretical methods, have been proven as powerful tools to perform biological network analysis. However, the majority of the developed descriptors and graph-theoretical methods does not have the ability to take vertex- and edge-labels into account, e.g., atom- and bond-types when considering molecular graphs. Indeed, this feature is important to characterize biological networks more meaningfully instead of only considering pure topological information. Results: In this paper, we put the emphasis on analyzing a special type of biological networks, namely biochemical structures. First, we derive entropic measures to calculate the information content of vertex- and edgelabeled graphs and investigate some useful properties thereof. Second, we apply the mentioned measures combined with other well-known descriptors to supervised machine learning methods for predicting Ames mutagenicity. Moreover, we investigate the influence of our topological descriptors - measures for only unlabeled vs. measures for labeled graphs - on the prediction performance of the underlying graph classification problem. Conclusions: Our study demonstrates that the application of entropic measures to molecules representing graphs is useful to characterize such structures meaningfully. For instance, we have found that if one extends the measures for determining the structural information content of unlabeled graphs to labeled graphs, the uniqueness of the resulting indices is higher. Because measures to structurally characterize labeled graphs are clearly underrepresented so far, the further development of such methods might be valuable and fruitful for solving problems within biological network analysis.


Related Articles

  • ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs.  // BMC Bioinformatics;2011 Supplement 6, Vol. 12 Issue Suppl 6, p332 

    The article offers information on the study conducted by the authors related to entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A G-protein coupled receptors (GPCRs). It states that GPCRs are involved in many different...

  • On the relationship between densities of Shannon entropy and Fisher information for atoms and molecules. Liu, Shubin // Journal of Chemical Physics;5/21/2007, Vol. 126 Issue 19, p191107 

    An analytical relationship between the densities of the Shannon entropy and Fisher information for atomic and molecular systems has been established in this work. Two equivalent forms of the Fisher information density are introduced as well. It is found that for electron densities of atoms and...

  • Computational study of cesium cation-humic substance interactions. A neutral analogue ligand molecules approach. Burk, Peeter; Tamp, Sven; Tammiku-Taul, Jaana; Maria, Pierre-Charles; Gal, Jean-Fran�ois // Proceedings of the Estonian Academy of Sciences, Chemistry;Jun2005, Vol. 54 Issue 2, p70 

    Interactions between the cesium cation (Cs+) and humic substances were studied by the calculations of complexes between Cs+ and small ligand molecules mimicking different moieties in humic substances. The cesium cation gas-phase affinities (CsCAs) and basicities (CsCBs) of 52 model compounds...

  • Synthesis of Azoles with Two Pyridine Substituents at Carbon Atoms and Their Use in Coordination Chemistry. (Review). Vatsadze, S.Z.; Nuriev, V.N.; Zyk, N.V. // Chemistry of Heterocyclic Compounds;Sep2005, Vol. 41 Issue 9, p1091 

    Published data on the synthesis of azoles containing two pyridine substituents are analyzed in relation to the type of central five-membered ring. The applications of such molecules as ligands in coordination chemistry are discussed.

  • Goud(I) komplekse van Bi- en multidentate P-N-ligande. Williams, D. B. G.; Traut, Telisha; Van Zyl, Werner E. // Suid-Afrikaanse Tydskrif vir Natuurwetenskap en Tegnologie;Jun2007, Vol. 26 Issue 2, p168 

    Ligands containing mixed hard-soft donor atoms and their metal complexes are enjoying significant interest at present. In this study, various P-N mixed-donor ligands were prepared from readily available starting materials and complexed to gold(I). Several new mono-gold complexes and two...

  • Free Energy of Ligand Binding to Protein: Evaluation of the Contribution of Water Molecules by Computational Methods. Cozzini, Pietro; Fornabaio, Micaela; Marabotti, Anna; Abraham, Donald J.; Kellogg, Glen E.; Mozzarelli, Andrea // Current Medicinal Chemistry;Dec2004, Vol. 11 Issue 23, p3093 

    One of the more challenging issues in medicinal chemistry is the computation of the free energy of ligand binding to macromolecular targets. This allows for the screening of libraries of chemicals for fast and inexpensive identification of lead compounds. Many attempts have been made and several...

  • Tight rigorous bounds to atomic information entropies. Angulo, J. C.; Dehesa, J. S. // Journal of Chemical Physics;11/1/1992, Vol. 97 Issue 9, p6485 

    The position-space entropy Sρ and the momentum-space entropy Sγ are two increasingly important quantities in the study of the structure and scattering phenomena of atomic and molecular systems. Here, an information-theoretic method which makes use of the Bialynicki–Birula and...

  • The Building Block of Life Cells, Molecules, Atoms, and Energy. Ann Foster, Mary // Massage & Bodywork;Jun/Jul2006, Vol. 21 Issue 3, p58 

    The article presents information on somatic anatomy related to quantum reality. Each body is composed of million of cells and cells are made of trillions of molecules. Sub-atomic particles are contained in an atom. The quantum body is dissolved into light and energy. The article also offers...

  • Composite Structural Motifs of Binding Sites for Delineating Biological Functions of Proteins. Kinjo, Akira R.; Nakamura, Haruki // PLoS ONE;Feb2012, Vol. 7 Issue 2, p1 

    Most biological processes are described as a series of interactions between proteins and other molecules, and interactions are in turn described in terms of atomic structures. To annotate protein functions as sets of interaction states at atomic resolution, and thereby to better understand the...


Read the Article


Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics