C581 1997 - Lecture 6:

Sequence Searching, Alignment, and Homology modeling

The UNIX Operating System
  1. UNIX Directory Structure and Files
  2. Useful Programs and Editors
  3. Useful UNIX Commands
Protein Data Bank (PDB)
  1. Link to the PDB Home Page
  2. PDB Searching
  3. PDB File Layout
  4. Retrieving PDB Files
  5. Adding hydrogens in INSIGHT
Sequence Searching and Alignment
  1. Protein Sequence Databases
  2. FASTA Format for Sequence Files:
  3. Searching for a Sequence Using Entrez
  4. Finding Homologous Sequences Using BLAST (blastp)
  5. Retrieving the Sequences Using Batch Entrez
  6. Aligning Sequences Using Clustal
  7. Alignment Editing
  8. Places To Look For Help
Homology Modeling
  1. Alignment of Known and Unknown Sequences
  2. Substitution of Coordinates for Conserved Regions
  3. Building in Loops and Closing Gaps
  4. Optimization of the Structure
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Last updated: 01/23/2001