5. Protein Structures, Geometry, and Topology

  1. Matthew He1 and
  2. Sergey Petoukhov2

Published Online: 12 OCT 2010

DOI: 10.1002/9780470904640.ch5

Mathematics of Bioinformatics: Theory, Practice, and Applications

Mathematics of Bioinformatics: Theory, Practice, and Applications

How to Cite

He, M. and Petoukhov, S. (2010) Protein Structures, Geometry, and Topology, in Mathematics of Bioinformatics: Theory, Practice, and Applications, John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470904640.ch5

Author Information

  1. 1

    Nova Southeastern University, Fort Lauderdale, Florida, USA

  2. 2

    Russian Academy of Sciences, Moscow, Russia

Publication History

  1. Published Online: 12 OCT 2010
  2. Published Print: 17 DEC 2010

Book Series:

  1. Bioinformatics: Computational Techniques and Engineering

Book Series Editors:

  1. Yi Pan and
  2. Albert Y. Zomaya

ISBN Information

Print ISBN: 9780470404430

Online ISBN: 9780470904640



  • computational geometry;
  • protein folding;
  • protein structure prediction;
  • protein unfolding


This chapter presents the basic concepts of geometry and topology, followed by protein primary structures, secondary structures, tertiary structure, and quaternary structure by geometric means. It discusses the classification of proteins, physical forces in proteins, protein motion (folding and unfolding), and basic methods (optimization and statistical methods) for secondary structure and tertiary structure prediction. Computational geometry can also be used as a tool for studying topology and architecture of macromolecules and macromolecular complexes. The chapter introduces briefly the common terms and algorithmic problems in computational geometry. It also talks about amino acids and present their three - dimensional geometric shapes. The objective of conformational search is to find all preferred conformations of a molecule. An alternative to conformational search is fold recognition.

Controlled Vocabulary Terms

computational geometry; proteins