PDBsum, one of the world’s foremost web sites for viewing and interrogating protein structures deposited in the Protein Data Bank (PDB), is now available as in-house product PDBsumProprietary, to allow companies to organise their internal proprietary protein structure data. PDBsum originated at University College London (UCL) in the Biomolecular Structure group. The system was developed by Dr. Roman Laskowski, now at the European Molecular Biology Laboratory’s European Bioinformatics Institute (EMBL-EBI) in Cambridge, UK.
PDBsumProprietary is a web-based system for organizing protein structural models, whether determined experimentally or theoretically. It presents a large number of structural analyses of the proteins, ligands, metals and/or DNA/RNA molecule(s) in the structure. The analyses are presented in largely self-explanatory schematic diagrams. These include PROCHECK analyses of the protein structure’s quality, PROMOTIF analyses of its secondary structural elements and motifs, LIGPLOT diagrams of protein-ligand interactions, NUCPLOT diagrams of protein-DNA interactions and protein-protein interaction diagrams. An analysis of the clefts in the structure reveals potential binding sites. Most of these analyses show the corresponding features in the 3D structure using the freely available molecular viewing programs RasMol and Jmol. In cases where the structure file contains the UniProt identifier, the coverage of the structure relative to the full length protein sequence is shown schematically, with links to other structures of the same protein. Links to relevant literature can be made if a structure’s “key reference” (ie the one describing its determination) is provided.
Pharmaceutical companies make extensive efforts to determine protein 3D structures in complex with small molecule compounds and increasingly, antibodies for rational drug design. The 3D models may either be experimental (x-ray or NMR derived) or homology models based on similarities to known experimental data. Much of this data is usually scattered around a research department, held in local directories etc. As a consequence data is often mislaid. A central in-house repository such as PDBsumProprietary would therefore safeguard this information for future research and enable comparative research to be carried out.
PDBsumProprietary requires the following software to either generate its analyses or to depict them:
RasMol - molecular graphics viewer
Jmol - java-based molecular graphics viewer
ImageMagick - image-package for creating/converting image files
PyMOL - molecular viewer for generating images of structures
Raster3D - suite for generating ray-traced images
wget/lynx - for downloading additional data from the web
To request this software, please check the box for the relevant licensing option in the left column, click the 'Add Licence(s) to Basket' button below and checkout from 'My Basket' in the top right corner of the page.