3. Graph Theoretic Models in Chemistry and Molecular Biology

  1. Amiya Nayak B.Math., Ph.D. Adjunct Research Professor Associate Editor Full Professor2 and
  2. Ivan Stojmenović Ph.D. Chair Professor founder editor-in-chief2,3
  1. Debra Knisley and
  2. Jeff Knisley

Published Online: 1 MAR 2007

DOI: 10.1002/9780470175668.ch3

Handbook of Applied Algorithms: Solving Scientific, Engineering and Practical Problems

Handbook of Applied Algorithms: Solving Scientific, Engineering and Practical Problems

How to Cite

Knisley, D. and Knisley, J. (2007) Graph Theoretic Models in Chemistry and Molecular Biology, in Handbook of Applied Algorithms: Solving Scientific, Engineering and Practical Problems (eds A. Nayak and I. Stojmenović), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470175668.ch3

Editor Information

  1. 2

    SITE, University of Ottawa, 800 King Edward Ave., Ottawa, ON K1N 6N5, Canada

  2. 3

    EECE, University of Birmingham, UK

Author Information

  1. Department of Mathematics, East Tennessee State University, Johnson City, TN 37614-0663, USA

Publication History

  1. Published Online: 1 MAR 2007
  2. Published Print: 14 FEB 2008

ISBN Information

Print ISBN: 9780470044926

Online ISBN: 9780470175668

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Keywords:

  • chemistry and molecular biology - graph theoretic models;
  • graph theoretic amino acid structure and QSAR arena;
  • machine learning and graphical invariants

Summary

The field of chemical graph theory utilizes simple graphs as models of molecules. These models are called molecular graphs, and quantifiers of molecular graphs are known as molecular descriptors or topological indices. Today's chemists use molecular descriptors to develop algorithms for computer aided drug designs, and computer based searching algorithms of chemical databases and the field is now more commonly known as combinatorial or computational chemistry. With the completion of the human genome project, related fields are emerging such as chemical genomics and pharmacogenomics. Recent advances in molecular biology are driving new methodologies and reshaping existing techniques, which in turn produce novel approaches to nucleic acid modeling and protein structure prediction. The origins of chemical graph theory are revisited and new directions in combinatorial chemistry with a special emphasis on biochemistry are explored. Of particular importance is the extension of the set of molecular descriptors to include graphical invariants. We also describe the use of artificial neural networks (ANNs) in predicting biological functional relationships based on molecular descriptor values. Specifically, a brief discussion of the fundamentals of ANNs together with an example of a graph theoretic model of RNA to illustrate the potential for ANN coupled with graphical invariants to predict function and structure of biomolecules is included.