Contents

• Introduction and Overview
  • Preface to Version 4.4 - Tom Walsh
  • Preface to Version 4.2 - Rob Russell
  • 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 interpreting structural similarities
  • The programs contained within the package
  
  
• Worked examples
  • Setup of examples
  • Multiple alignment using an initial multiple sequence alignment
  • Database Scanning
  • Using SCAN mode as the starting point for multiple alignment
  • Generating a set of superimposed structues
  • Alignment without an initial multiple alignment using ROUGHFIT
  • Protein domain databases
  • Generating transformed coordinates using TRANSFORM
  • 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 STAMP database scanning mode
  • 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 using ACONVERT
  
  
• Installation
  • Compiling/running
  • Configuring STAMP
  • Getting other programs
  
  
• Some of our studies involving STAMP
• Bibliography