PepcDB | Data Preparation, Validation, and Deposition

Last updated June 27, 2008

1.  Retrieve required data items from your local database or laboratory management system (LIMS).

The following are the core blocks of information that should be included into the PepcDB data file:

• A list of protein sequences or targets selected for structure determination and/or functional characterization by your laboratory. Each protein sequence should be associated with the data items including protein name, source organism, and reference to external databases such as Uniprot, Genbank, PFAM, etc.


• All experimental protocols used in production or functional studies of proteins deposited to PepcDB.


• Contact information of people who performed the experiments including name, laboratory affiliation, and e-mail address.


• All experimental trials should be deposited to PepcDB. This includes both successful and failed experiments. The experimental trials may represent:
  • analytical or large scale trials
  • cloning of a target sequence into different plasmid vectors
  • expression of a target protein in different expression systems
  • different purification pipelines
  • various crystallization or NMR conditions
• Every experimental trial should be associated with status history showing the dates when experiment was initiated and completed.

2.  Assemble your data into XML format according to PepcDB schema specifications. To help you to assemble your data into PepcDB data file the following documents are provided:

• Detailed description of the PepcDB content
• PepcDB schema diagram
• PepcDB XML schema specification

3.  Confirm that your data file is consistent with PepcDB specifications using PepcDB validation tool. Your validated PepcDB data file will be deposited to the PepcDB.

4.  If you have any question regarding to the data deposition to PepcDB please contact: target-help@deposit.rcsb.org .