166301 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education


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)

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