Prediction of Protein Structure and the Principles of Protein Conformation

1. Front Matter

   Pages i-xiii

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2. Principles and Patterns of Protein Conformation

   • Jane S. Richardson, David C. Richardson

   Pages 1-98

3. The Structure of the Photochemical Reaction Center of Rhodopseudomonas viridis and Its Implications for Function

   • Johann Deisenhafer, Robert Huber, Harmut Michel

   Pages 99-116

4. Virus Structure

   • Gerald Stubbs

   Pages 117-148

5. Protein Stability and Function

   • J. Andrew McCammon, Chung F. Wong, Terry P. Lybrand

   Pages 149-159

6. Stabilization Energies of Protein Conformation

   • Tom Alber

   Pages 161-192

7. The Development of the Prediction of Protein Structure

   • Gerald D. Fasman

   Pages 193-316

8. The Role of Energy Minimization in Simulation Strategies of Biomolecular Systems

   • D. H. J. Mackay, A. J. Cross, A. T. Hagler

   Pages 317-358

9. The Role of Electrostatic Interactions in the Structure of Globular Proteins

   • Neil K. Rogers

   Pages 359-389

10. Chou-Fasman Prediction of the Secondary Structure of Proteins

    • Peter Prevelige Jr., Gerald D. Fasman

    Pages 391-416

11. The GOR Method for Predicting Secondary Structures in Proteins

    • J. Garnier, B. Robson

    Pages 417-465

12. Prediction of Packing of Secondary Structure

    • Kozo Nagano

    Pages 467-548

13. Prediction of Protein Structural Classes from Amino Acid Compositions

    • Peter Y. Chou

    Pages 549-586

14. Use of Class Prediction to Improve Protein Secondary Structure Prediction

    • Gilbert Deléage, Bernard Roux

    Pages 587-597

15. Redundancies in Protein Sequences

    • Russell F. Doolittle

    Pages 599-623

16. The Hydrophobicity Profile

    • George D. Rose, Jonathan E. Dworkin

    Pages 625-633

17. Hydrophobic Moments as Tools for Analyzing Protein Sequences and Structures

    • David Eisenberg, Morgan Wesson, William Wilcox

    Pages 635-646

18. Tertiary Structure Prediction

    • Fred E. Cohen, Irwin D. Kuntz

    Pages 647-705

19. Structure Prediction for Membrane Proteins

    • Fritz Jähnig

    Pages 707-717

20. Identification of Membrane Proteins and Soluble Protein Secondary Structural Elements, Domain Structure, and Packing Arrangements by Fourier-Transform Amphipathic Analysis

    • Janet Finer-Moore, J. Fernando Bazan, John Rubin, Robert M. Stroud

    Pages 719-759

The prediction of the conformation of proteins has developed from an intellectual exercise into a serious practical endeavor that has great promise to yield new stable enzymes, products of pharmacological significance, and catalysts of great potential. With the application of predic­ tion gaining momentum in various fields, such as enzymology and immunology, it was deemed time that a volume be published to make available a thorough evaluation of present methods, for researchers in this field to expound fully the virtues of various algorithms, to open the field to a wider audience, and to offer the scientific public an opportunity to examine carefully its successes and failures. In this manner the practitioners of the art could better evaluate the tools and the output so that their expectations and applications could be more realistic. The editor has assembled chapters by many of the main contributors to this area and simultaneously placed their programs at three national resources so that they are readily available to those who wish to apply them to their personal interests. These algorithms, written by their originators, when utilized on pes or larger computers, can instantaneously take a primary amino acid sequence and produce a two-or three-dimensional artistic image that gives satisfaction to one's esthetic sensibilities and food for thought concerning the structure and function of proteins. It is in this spirit that this volume was envisaged.

• Amino acid
• Peptide
• development
• enzymes
• protein
• protein folding
• proteins

• Graduate Department of Biochemistry, Brandeis University, Waltham, USA

  Gerald D. Fasman

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