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The Protein Folding Problem and Tertiary Structure Prediction pp 507–548Cite as

Toward Quantitative Protein Structure Prediction

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Abstract

We review a constrained optimization strategy known as the antlion method for the purpose of protein structure prediction. This method involves the use of neural network predictions of secondary and tertiary structure to systematically deform a protein energy hypersurface to retain only a single minimum near to the native structure. Successful constrained optimization as applied to protein folding relies on (1) an understanding of the chemistry that distinguishes the native minimum from other metastable structures, (2) the incorporation of such information as robust constraints on the energy function to isolate the native structure minimum, and (3) progress toward providing a quantitative representation of the potential or free energy function. We provide a discussion of completed work by us that begins to affect these three problem areas as we move toward our goal of quantitative protein structure prediction.

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Authors
  1. Teresa Head-Gordon
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Editors and Affiliations

  1. Department of Chemistry, The Pennsylvania State University, 152 Davey Laboratory, University Park, PA, 16802-6300, USA

    Kenneth M. Merz Jr.  & Scott M. Le Grand  & 

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© 1994 Birkhäuser Boston

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Head-Gordon, T. (1994). Toward Quantitative Protein Structure Prediction. In: Merz, K.M., Le Grand, S.M. (eds) The Protein Folding Problem and Tertiary Structure Prediction. Birkhäuser Boston. https://doi.org/10.1007/978-1-4684-6831-1_15

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  • DOI: https://doi.org/10.1007/978-1-4684-6831-1_15

  • Publisher Name: Birkhäuser Boston

  • Print ISBN: 978-1-4684-6833-5

  • Online ISBN: 978-1-4684-6831-1

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