Table of Contents for: Pedestrian guide to analysing sequence databases

¹ EMBL, 69012 Heidelberg, Germany;
²EBI, Hinxton Hall, Hinxton, Cambridge CB10 1RQ, England

e-mail: rost@embl-heidelberg.de and schneider@embl-heidelberg.de

• Abstract
• Introduction
• State of the art in predicting protein structure and function
  • Sequence-structure gap
  • Predicting protein structure in 3D
  • Predicting protein structure in 1D
  • Predicting protein function
• Getting access to databases and services
  • Surfing on the World Wide Web
  • Public databases
  • General services
• Searching for homologues
  • Getting alignments
  • Principles of alignment methods
• • Getting predictions for protein structure
  • Principles of structure prediction
• Avoiding common traps of sequence analysis
  • Pitfalls of sequence alignments
  • Pitfalls of 1D structure prediction
  • Pitfalls of 3D structure prediction
  • How to separate the chaff from the wheat?
• Conclusions
• References
• Tables
  • Table 1: Abbreviations and technical terms ( separate window )
  • Table 2: Rules of thumb for sequence analysis ( separate window )
• Figures
  • Fig. 1: Representation of HIV protease (PDB code 1hiv) in 1D and 3D ( separate window )
  • Fig. 2: Protein sequences for which 3D structure can be predicted ( separate window )
  • Fig. 3: Coverage of homology modelling vs. sequence identity ( separate window )