135787 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

This site is used for testing new functionality and bug fixes. Things may not always work the way you expect. For the production site, please go to http://www.rcsb.org


RCSB PDB Protein Comparison Tool


Calculate pairwise sequence or structure alignments.

Alignment Options

Align custom files (Launches a Java Web Start application)

Show Example (4HHB.A vs 4HHB.B Java-FATCAT, rigid)

More documentation on the RCSB PDB protein structure alignments

Compare the following two proteins  
ID 1:
ID 2:

To find the proteins you want to align you can use the auto-suggest feature. It supports searching by
  • PDB ID (e.g. 1cdg)
  • SCOP ID (e.g. d1cdga1)
  • SCOP classification ID (e.g. b.1.18)
  • SCOP stable ID (e.g. 21816)
  • text search (based on SCOP descriptions)

If you are having problems launching Java Web Start applications, view our troubleshooting Java Web Start page for more help.