Bioinformatics Bioinformatics Tool Structure Analysis

AutoDep

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AutoDep is a web-based system for the deposition and validation of large macromolecular structures including proteins and ligand-binding structures.

AutoDep was developed by the Protein Data Bank at Brookhaven National Laboratory (BNL) as a flexible and portable system that has already been adopted by other primary databases and used on different operating systems. AutoDep was introduced at BNL in 1996.

Features

  • The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators for the complete and accurate description of the structural experiment and its results. 
  • AutoDep moves the burden of unexciting data-formatting issues to computer programs, freeing the researcher who had been studying the protein’s structure to focus on the completeness and accuracy of the structural entry and enabling the PDB’s professional staff to deal with issues of representation and curation of the data. 
  • AutoDep also provides interactive feedback to the depositor, so that any errors or inadequacies of the data may be addressed immediately. 

The new system includes various features that improve the quality of the final data which are deposited into the PDB. The interface definitions include validation patterns that are automatically applied to user-supplied data as they are entered, allowing a first round of data validation to be applied even as data are entered into the system. Once deposition is complete, but before submission, a suite of analysis programs are run, providing a further layer of validation for structures. Major problems in the uploaded coordinates are often identified at this stage of the deposition process, allowing the depositor to correct their data themselves, usually without intervention from AutoDep maintainers.

The AutoDep system uses a client-server architecture running over the World Wide Web (WWW). HyperText Markup Language (HTML) forms are generated at the server side and sent to the user’s site. On the user, or client side, depositors use their favorite web browser to access and complete the forms, then send their data through the Common Gateway Interface (CGI) to the server. The server’s application programs process the information and send the results back to the users, again through their web browser. Therefore, AutoDep may be viewed using a browser of the user’s choosing no matter which computer platform is used, resulting in a shallow learning curve. Researchers use web forms to submit their data over the web quickly and easily. 

AutoDep is integrated into the PDB’s validation suite, which includes PDB-developed checking programs and the WHAT_CHECK implementation of the WHAT IF suite. After passing completeness and syntax checking, submitted data are checked against these programs and generated reports are returned to the depositor over the web. AutoDep may be easily integrated with other commonly used structural validation programs.

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