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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
Geoff Barton
1999-04-16