Multiple Alignment aligns multiple proteins of the same structural class using the STAMP program, courtesy of R.B. Russell and G.J. Barton. By utilizing the graphical features of VMD, (i.e. 3D OpenGL Display, Graphical Representations), and its own features, (i.e. Sequence Display, Molecule Coloring, Residue Selection, and Phylogenetic Tree), Multiple alignment explores the sequence and structure of multiple aligned proteins concurrently. The plugin was created primarily to meet the research needs of biomedical scientists desiring "to study the evolutionary changes in sequence and structure of proteins across all three domains of life."

Articles

The comparative sequence and structure metrics and analysis tools of Multiple Alignment are availble in the following articles,

Tutorials and Documentation

Please note:
This tool is designed for evolutionary analysis on a single protein domain. You may be able to to compare multi-domain proteins provided chain A is similar in all structures. Please be aware that attempting to align dissimilar structures or multichain proteins may cause the alignment procedure to hang, and eventually fail.