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Protein structure prediction : a practical approach /

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Bibliographic Details
Other Authors: Sternberg, Michael J. E.
Format: Book
Language:English
Published: Oxford ; New York : IRL Press at Oxford University Press, [1996]
Series:Practical approach series ; 170.
Subjects:
Protein Conformation.
Amino Acid Sequence.
Computer Simulation.
Table of Contents:
  • 1. Protein structure prediction - principles and approaches
  • Introduction
  • Dominant effects in protein folding
  • Analyses of protein structure
  • Sequence analysis
  • Secondary structure prediction
  • Tertiary structure prediction
  • Simulations with protein structures
  • Conclusion
  • 2. Protein sequence alignment and database scanning
  • Introduction
  • Amino acid scoring schemes
  • Comparison of two sequences
  • Evaluation of alignment accuracy
  • Multiple sequence alignment
  • Database scanning
  • Summary
  • 3. Identification of protein sequence motifs
  • Introduction
  • Identification of protein sequence motifs
  • Pattern extraction
  • Summary
  • 4. Prediction of secondary structure
  • Introduction : the need for secondary structure prediction
  • Methods of secondary structure prediction
  • Evaluating prediction methods
  • A practical example
  • Recommendations
  • Conclusions
  • 5. Prediction of transmembrane protein topology
  • Introduction
  • Structural classes : helix bundles and β-barrels
  • Membrane insertion : setting-up the topology
  • Prediction of transmembrane helics and membrane topology
  • Prediction of transmembrane β-strands
  • 6. Comparative modelling of proteins
  • Introduction
  • Different approaches to comparative modelling
  • Accuracy of models and evaluation of models
  • Use of protein models and summary comments
  • 7. Antibody combining sites : structure and prediction
  • Introduction
  • Antibody structure
  • Variable region modelling
  • Accuracy, limitations, and future developments
  • Applications
  • Future prospects
  • 8. Protein folds and their recognition from sequence
  • Introduction
  • Fold libraries
  • Evaluating structural models
  • Rold recognition methods
  • Case study
  • The asilomar competition
  • Software availability
  • Conclusions and future directions
  • 9. The combinatorial approach
  • Introduction
  • Secondary structure prediction with tertiary intent
  • Tertiary structure from secondary structure
  • Sorting between alternative models
  • Conclusion
  • 10. Modelling protein conformation by molecular mechanics and dynamics
  • Introduction
  • Methods
  • Applications
  • Summary
  • 11. Docking ligands to proteins
  • Introduction
  • Docking programs
  • Preparing your input
  • Docking a small molecule to a protein
  • Docking a protein ligand to a protein receptor
  • Novel inhibitor discovery
  • 12. The prediction challenge