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structural biology | BioMedBridges

structural biology

Determine the coordination geometry of metals in biological macromolecules

Metals are essential for the structure and function of many proteins and nucleic acids. The geometric arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. FindGeo quickly finds and determines the coordination geometry of selected, or all, metals in a given structure.

Unlocking biomolecule volume data

Information on the structure of macromolecules is important for biology and medicine because the function of many important biological processes can be directly linked to macromolecular structure or changes therein. For example, structural information on how a drug is bound to a target may yield vital clues on how to optimize its structure to promote more efficient binding. The BioMedBridges shape-matching software - which will be incorporated into a web-based shape-matching service - will enable the wealth of low-resolution volume data in the EMDB and PDB resources to be searched based on their shape, providing entirely new perspectives on the relationships between structures.

Sharing protein engineering knowledge


PiMS is a laboratory information management system for use in recombinant protein production laboratories; to manage the stages from the selected target protein to the production of soluble protein. PiMS development is part of a larger vision to provide a unified and extensible set of software tools for structural biology, offering seamless data transfer and a consistent user experience, from target selection to the interpretation of the structure.

Final version of the web-based shape-matching service

A software pipeline named SMaSB was previously developed to perform the volume/shape matching that underpins the set of tools being developed in WP9. These tools are novel in providing access to a growing class of structural biology data viz. volume data. The SMaSB software is primarily a set of Python codes which organise the metadata, control the data flow during volume/shape matching, and record the results. Third-party software is called to perform the compute-intensive steps in the pipeline. The first full version of SMaSB was released in December 2014, and reported in Deliverable 9.1. We now report on the associated web service (PDBeShape) which provides a user-friendly front-end to SMaSB results. It provides web access to a curated database of structural volumes, derived from deposited structures in the Electron Microscopy Data Bank (EMDB) and Protein Data Bank (PDB), together with pre-processed alignments and scores. We have made the first version of the PDBeShape service publically available at Here we give details on the current functionality of PDBeShape and the technical underpinning. More extensive documentation is provided on the web page.
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