Molecular Modeling: Mapping Biochemical State Space

  • Peter R. Bergethon


At this point in our journey we should generally agree about the central element of biophysical chemical study: The important biological observables of function and action in a biological state space are a direct consequence of the coordinate structure of the physical elements (mass, energy, and forces) of biomolecules. We have used this concept to construct potential energy surfaces that connect the position of the physical elements in space with a measurable interaction (i.e., force or energy). How this helps us with our interest in function is as follows: The observed function of a system is simply its perceived interaction with elements within the system and with the observer (whether strongly or weakly coupled to the system). All interactions require energy. If no force or action is exerted between elements of a system, the system can have no function. Furthermore, if no force is exerted by the system on the observer, it is impossible to assign function to the system.


Force Field Harmonic Function Molecular Modeling Potential Energy Surface Empirical Method 
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Further Reading


  1. HyperChem® computational chemistry: Molecular visualization and simulation. (1994). Hypercube, Inc. Publication HC40–00–03–00. Tutorial to one of the widespread, popular, PC–based, all–in–one programs. Gives a generally useful review of the field of computational chemistry.Google Scholar
  2. Lipkowitz K. B., Boyd D. B., eds. (1990) Reviews in Computational Chemistry. VCH Publishers, New York. A set of review articles covering the field of computational chemistry. A good place to start further investigation of the field. There are annual volumes with this name.Google Scholar

Force Fields

  1. Berkert U., and Allinger N. L. (1982) Molecular mechanics. American Chemical Society Monograph 177. Washington, D.C. The classic introduction to force-field methods.Google Scholar
  2. Boyd D. B., and Lipkowitz, K. B. (1982) Molecular mechanics. The method and its underlying philosophy. J. Chem. Ed., 59: 269–74.CrossRefGoogle Scholar
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Quantum Mechanical Methods

  1. Hinchcliffe A. (1988) Computational Quantum Chemistry. John Wiley and Sons, New York.Google Scholar

Dynamical Modeling

  1. Daggett V., and Levitt M. (1993) Realistic simulations of native-protein dynamics in solution and beyond. Ann. Rev. Biophys. Biomol. Struct., 22: 353–80.CrossRefGoogle Scholar
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Secondary Structure Prediction

  1. Chou P. Y., and Fasman G. D. (1978) Prediction of the secondary structure of proteins from their amino acid sequence. Advances in Enzymology, 47: 45–148.Google Scholar
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  3. Gilbert R. J. (1992) Protein structure prediction from predicted residue properties utilizing a digital encoding algorithm. J. Mol. Graphics, 10: 112–19.CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 1998

Authors and Affiliations

  • Peter R. Bergethon
    • 1
  1. 1.Department of BiochemistryBoston University School of MedicineBostonUSA

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