Introduction

3D Blocks is a search and display tool which allows you to view blocks on a protein structure. It uses a Blocks family (either from the Blocks database or supplied by the user) as the query sequence for a MAST search of the PDB. It then determines which regions on the high-scoring protein sequences correspond to the blocks, and creates output files to display its results. These output files are in several formats: HTML/Chime, MolScript, RasMol, and the PDB viewer.

To speed processing, we can do an initial BLAST search of the PDB using a protein sequence, and run MAST only on highscoring sequences. This option is only available if you are using Blocks from the Blocks database, or have provided a sequence similar to or contained in your own Blocks.

A word of caution: MAST searches may result in false-positive hits, so please use care in determining whether each hit is actually valid.