Atomistic vs. Continuous Representations in Molecular Biology

  • David S. Goodsell


Representations used in science may be separated into two classes: atomistic representations, which model discrete entities interacting through pair-wise forces, and continuous representations, which model derived properties that vary continuously through space. The choice of an atomistic or a continuous model is governed primarily by the complexity of the system: atomistic models are useful in systems with several thousand interacting entities, whereas continuous models are necessary in larger systems. In molecular biology, atomistic models are used at two levels: at the atomic level, where the atomic structure of molecules is studied, and at the molecular level, where the molecular structure of cells is studied. Continuous models are also useful at both levels, for simplifying the atomic details of large, complex molecules, and for simplifying the molecular details of entire cells.


Continuous Model Continuous Representation Atomistic Model Individual Molecule Scale Domain 
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.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Goodsell DS and Olson AJ. Soluble proteins: size, shape and function. Trends Biochem. Sci. 1993; 18:65–68.CrossRefGoogle Scholar
  2. 2.
    Richardson JS. The anatomy and taxonomy of protein structure. Adv. Protein Chem. 1981; 34:167–339.CrossRefGoogle Scholar
  3. 3.
    Lee B and Richards FM. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 1971; 55:379–400.CrossRefGoogle Scholar
  4. 4.
    Fulton AB. How crowded is the cytoplasm? Cell 1982; 30:345–347.CrossRefGoogle Scholar
  5. 5.
    Zimmerman SB and Minton AP. Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu. Rev. Biophys. Biocool. Struct. 1993; 22:27–65.CrossRefGoogle Scholar
  6. 6.
    Minton AP. Macromolecular crowding and molecular recognition. J. Mol. Recognition 1993; 6:211–214.CrossRefGoogle Scholar
  7. 7.
    Guttman HJ, Anderson CF and Record MT. Analysis of thermodynamic data 155 for concentrated hemoglobin solutions using scaled particle theory: implications for a simple two-state model of water in thermodynamic analyses of crowding in vitro and in vivo. Biophys. J. 1995; 68:835–846.CrossRefGoogle Scholar
  8. 8.
    Blattner FR, Plunkett G, Bloch CA, et al. The complete genome sequence of Escherichia coli K-12. Science 1997; 277:1453–1462.CrossRefGoogle Scholar
  9. 9.
    VanBogelen RA, Sankar P, Clark RL, Bogan JA and Neidhardt FC. The gene-protein database of Escherichia coli: edition 5. Electrophoresis 1992; 13:1014–1054.CrossRefGoogle Scholar
  10. 10.
    Goodsell DS. Inside a living cell. Trends in Biochem. Sci. 1991; 16(6):203–206.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag London 1999

Authors and Affiliations

  • David S. Goodsell
    • 1
  1. 1.Department of Molecular BiologyThe Scripps Research InstituteLa JollaUSA

Personalised recommendations