Contents

• Contents
• Introduction and Overview
  • Preface to Version 4.2
  • Overview
  • Background
  • A brief description of the package
    • Initial superimposition
    • Pairwise comparisons and alignments (PAIRWISE)
    • Multiple alignment (TREEWISE)
    • Structure database scanning (SCAN)
    • Displaying STAMP output (VER2HOR, DSTAMP, GSTAMP)
  • Some comments on interperetting structural similarities
  • The programs contained within the package
• Worked examples
  • Multiple alignment (PAIRWISE and TREEWISE)
  • Alignment using an initial rough superimposition
  • Database Scanning
  • Using scans as a starting point for multiple alignment
  • Protein domain databases
  • Generating transformed coordinates
  • Generating averaged coordinates
  • Displaying/processing the output
    • POSTSTAMP
    • STAMP_CLEAN
    • Displaying text alignments
    • Pretty Alignments via ALSCRIPT
    • Pretty Structures via MOLSCRIPT
• Input and Output format for all programs
  • Describing domain structures
  • Transformations
  • Sequence format
  • Multiple alignment format
  • Output from SCANS
  • Output to standard output or log file
• Summary of STAMP parameters
  • Main program (STAMP)
  • Summary of parameters for other programs
    • PDB checker (PDBC)
    • PDBSEQ
    • ALIGNFIT
    • VER2HOR
    • DSTAMP
    • SORTTRANS
    • TRANSFORM
    • PICKFRAME
    • MERGETRANS & EXTRANS
    • MERGESTAMP
    • AVESTRUC
    • GSTAMP
    • STAMP_CLEAN
    • Converting alignment formats ACONVERT
• Installation
  • Compiling/running
  • Setting up STAMP files
  • Getting other programs
• Some of our studies involving STAMP
• Appendix - STAMP Academic License
• Bibliography