The Protein Folding Problem and Tertiary Structure Prediction

1. Front Matter

   Pages i-x

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2. Modeling Side Chains in Peptides and Proteins with the Locally Enhanced Sampling/Simulated Annealing Method

   • Adrian Roitberg, Ron Elber

   Pages 1-41

3. Conformation Searching Using Simulated Annealing

   • Stephen R. Wilson, Weili Cui

   Pages 43-70

4. Multiple-Start Monte Carlo Docking of Flexible Ligands

   • Trevor N. Hart, Randy J. Read

   Pages 71-108

5. The Genetic Algorithm and Protein Tertiary Structure Prediction

   • Scott M. Le Grand, Kenneth M. Merz Jr.

   Pages 109-124

6. Conformational Search and Protein Folding

   • Robert E. Bruccoleri

   Pages 125-163

7. Building Protein Folds Using Distance Geometry: Towards a General Modeling and Prediction Method

   • William R. Taylor, András Aszódi

   Pages 165-192

8. Molecular Dynamics Studies of Protein and Peptide Folding and Unfolding

   • Amedeo Caflisch, Martin Karplus

   Pages 193-230

9. Contact Potential for Global Identification of Correct Protein Folding

   • Gordon M. Crippen, Vladimir N. Maiorov

   Pages 231-277

10. Neural Networks for Molecular Sequence Classification

    • Cathy H. Wu

    Pages 279-305

11. The “Dead-End Elimination” Theorem: A New Approach to the Side-Chain Packing Problem

    • Johan Desmet, Marc De Maeyer, Ignace Lasters

    Pages 307-337

12. Short Structural Motifs: Definition, Identification, and Applications

    • Ron Unger

    Pages 339-351

13. In Search of Protein Folds

    • Manfred J. Sippl, Sabine Weitckus, Hannes Flöckner

    Pages 353-407

14. An Adaptive Branch-and-Bound Minimization Method Based on Dynamic Programming

    • Sandor Vajda, Charles Delisi

    Pages 409-432

15. Computational Complexity, Protein Structure Prediction, and the Levinthal Paradox

    • J. Thomas Ngo, Joe Marks, Martin Karplus

    Pages 433-506

16. Toward Quantitative Protein Structure Prediction

    • Teresa Head-Gordon

    Pages 507-548

17. The Role of Interior Side-Chain Packing in Protein Folding and Stability

    • James H. Hurley

    Pages 549-578

18. Back Matter

    Pages 579-581

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A solution to the protein folding problem has eluded researchers for more than 30 years. The stakes are high. Such a solution will make 40,000 more tertiary structures available for immediate study by translating the DNA sequence information in the sequence databases into three-dimensional protein structures. This translation will be indispensable for the analy­ sis of results from the Human Genome Project, de novo protein design, and many other areas of biotechnological research. Finally, an in-depth study of the rules of protein folding should provide vital clues to the protein fold­ ing process. The search for these rules is therefore an important objective for theoretical molecular biology. Both experimental and theoretical ap­ proaches have been used in the search for a solution, with many promising results but no general solution. In recent years, there has been an exponen­ tial increase in the power of computers. This has triggered an incredible outburst of theoretical approaches to solving the protein folding problem ranging from molecular dynamics-based studies of proteins in solution to the actual prediction of protein structures from first principles. This volume attempts to present a concise overview of these advances. Adrian Roitberg and Ron Elber describe the locally enhanced sam­ pling/simulated annealing conformational search algorithm (Chapter 1), which is potentially useful for the rapid conformational search of larger molecular systems.

• DNA
• biology
• genome
• molecular biology
• protein
• protein structure
• protein structure prediction
• tertiary structure
• translation

• Department of Chemistry, The Pennsylvania State University, University Park, USA

  Kenneth M. Merz, Scott M. Grand

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