next up previous contents
Next: Background Up: Introduction and Overview Previous: Preface to Version 4.2   Contents

Overview

STAMP is a package for the alignment of protein sequences based on three-dimensional (3D) structure. It provides not only multiple alignments and the corresponding `best-fit' superimpositions, but also a systematic and reproducible method for assessing the quality of such alignments. It also provides a method for protein 3D structure data base scanning. In addition to structure comparison, the STAMP package provides input for programs to display and analyse protein sequence alignments and tertiary structures. Please note that, although STAMP outputs a sequence alignment, it is a program for 3D structures, and NOT sequences. If you are after a multiple sequence alignment for proteins of unknown 3D structure, stop reading now and contact GJB for information about AMPS, which can be used to perform multiple sequence alignments, or see www.jalview.org for GJB's latest methods for this problem.

Comparison of 3D structures is a complicated business, particularly if one wants to do unusual things (i.e. reverse a strand direction, swap two segments of a structure around, only consider equivalent structures of greater than 10 residues, etc.). Complicated things are possible with STAMP but as a consequence, the method is very complex. Please be patient, and read this manual carefully.

Alternatively, if you only want to do fairly straightforward things, such as align a set of structures or search a database of structures for similarities, you can skip the remainder of this chapter and go straight to the next one (Chapter: 2), which contains a few worked examples that should demonstrate how to use STAMP in a black-box way.


next up previous contents
Next: Background Up: Introduction and Overview Previous: Preface to Version 4.2   Contents