Download 3D Protein Structure Database

This tool downloads the 3D Protein Structure Database from a public accessible HTTP location hosted by QIAGEN Aarhus.

The database contains a curated set of sequences with known 3D structures, which are obtained from the Protein Data Bank ( [Berman et al., 2003]. The information stored in the database (e.g. protein sequence, X-ray resolution) is used to identify suitable structural templates when using the Link Variants to 3D Protein Structure tool.

To download the database, select:

        Toolbox | Resequencing Analysis (Image track_tools) | Functional Consequences (Image folder) | Download 3D Protein Structure Database (Image download_variantsin3d_16_n_p)

If you are connected to a server, you will first be asked about whether you want to download the data locally or on a server. In the next wizard step you are asked to select the download location (see figure 27.85).

Image download_3D_protein_database_step2_gwb
Figure 27.85: Select the download location.

The downloaded database will be installed in the same location as local BLAST databases (e.g. <username>/CLCdatabases) or at a server location if the tool was executed on a CLC Server. From the wizard it is possible to select alternative locations if more than one location is available.

When new databases are released, a new version of the database can be downloaded by invoking the tool again (the existing database will be replaced).

If needed, the Manage BLAST Databases tool can be used to inspect or delete the database (the database is listed with the name 'ProteinStructureSequences'). You can find the tool here:

        BLAST (Image blastsearch)| Manage BLAST Databases (Image blast_databases_16_n_p)