We hope that you will find 3D-Blast is easy to use. However, please remember that 3D-Blast was designed to work with individual protein domains. It is not suitable for comparing multi-domain or multi-chain proteins.

In general, PDB files may be downloaded from the RCSB Protein Data Bank. Before submiting a job, it is usually a good idea to examine your PDB files using a visualisation tool such as Hex or Jmol, and then to use a text editor to delete any duplicate domains or unwanted atoms.

Superposing and aligning two structures
Several pairs of structures which are difficult to align using conventional structural alignment tools have been compiled by Manfred Sippl and Markus Wiederstein. The following two protein pairs correspond to their cases:
Case C: 1EUD (Chain A, Domain 1), 1EUD (Chain A, Domain 2)
Case E: 1TE2 (Chain B, Domain 2), 1ZOL (Chain A, Domain 2)

These examples may be downloaded and given as the fixed and moving input files for superposing by 3D-Blast. The full set of 12 examples from Mavridis et al., 2011 can be downloaded here.

Searching the CATH database
These above examples may also be used individually to search the CATH database. However, since this involves searching some 12,881 structures please remember that this could take several minutes.

Accessing your results
After you have uploaded a structure to 3D-Blast, you are provided with a link from which you can access a results page. The results of each run of 3D-Blast is available for 24 hours. If you provide an email address, you will also be notified of the results link when your query has finished.

All data is stored on the server anonymously using random numbers. Unless there is a problem with the operation of the server, we will not look at your data or use your email address.

3D-Blast version July 2011