Welcome to 3D Protein Lab

The goal of this project is to allow you to search through the PDB database of protein structures using a combination of sequence and structure constraints. We have developed a pattern syntax that is an extension of the PROSITE pattern syntax. The sequence components are defined using the PROSITE pattern syntax, and the structural features are implemented using our own syntax. Please see the help page for a description of all the elements of the expression language. The search language and engine are described in our forthcoming publication

Hawkins & Pisabarro (2010). 3D Regular Expressions for Protein Structure Search. (In Preparation).

To see an example of the results returned by 3D Protein Lab, load this example and run the query engine. This text will be replaced with the matching structures. Experiment with modifying the pattern to see how the results change.

Please Note As the query language is open, the amount of time that is required to run a query can vary dramatically. The query status bar cannot start to show progress until after the SQL has returned the initial list of potential matches. We recommend that you include some specific residues in the pattern, and try and make the sequence components as long as possible. This will severely decrease the number of potential matches that need to be evaluated.