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Molecular Modeling: Mapping Biochemical State Space

  • Peter R. Bergethon

Abstract

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.

Keywords

Force Field Harmonic Function Molecular Modeling Potential Energy Surface Empirical Method 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Further Reading

General

  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

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Quantum Mechanical Methods

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Dynamical Modeling

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Secondary Structure Prediction

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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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