1) The system supports two types of query methods: Query by PDB ID and Query by Protein Chain Structure.
For PDB with known ID, input PDB ID and Chain ID and click Verify button.
For ODB with unknown ID, click radio button Unknown Protein Chain Structures, click Browse button to select PDB file, then click Upload button to upload the PDB file to the server. Finally, click Verify button.
2) For Query by Protein Chain Structure, click chain ID to submit. While for Query by PDB ID, just click Submit button.
3) The retrieval result is shown in the following figure. The top left panel shows a superimposed view of a query protein chain and a selected result chain from the ranked list in the top right panel. The backbone of query and result protein is represented by orange and lightblue, respectively. Users can check Result Protein and/or Query Protein to view the retrieved chain and/or the query chain. By clicking on a hyperlink below the top left panel, users can view different display themes. The lower panel displays the structure alignment results represented by sequences with the RMSD and alignment length.
Any problem, please send email to Admin.
 C.R.Shyu, P.H.Chi , G.Scott, D.Xu. ProteinDBS: a real-time retrieval system for protein structure comparison Nucleic Acids Research , Vol. 32, Jul.2004: w572 - 575. [PDF]