Structural Bioinformatics Group
Division of Molecular Biosciences
Faculty of Natural Sciences

Servers, Software & Databases

This is a list of our currently available servers, software & databases.


    Global and Restrained Docking Exploration Nexus

    3D-GARDEN is a state-of-the-art comprehensive software suite and server for protein-protein docking with full high-performance computing functionality implementing multiple novel efficient methodologies:

    • TODE, using simplicial complex representation of the protein surfaces to generate and score an ensemble of complexed structures in the initial conformational state, which is naturally pre-enriched in structures with favourable shape complementarity

    • RABBIT, an efficient refinement method based on exhaustive search of torsion angles with tuned step sizes

    Please note that this program supersedes 3D-DOCK.

  • 3D-GENOMICS (Academic use only)

    A database for protein structure and function annotation across different genomes.

  • 3D-PSSM (Academic use only)

    Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure and solvation potential information.

  • ConFunc

    Sequence based protein function predictions using Gene Ontology

  • Genome Assignments

    Structural assignments for the Mycoplasma genitalium and Mycobacterium tuberculosis genomes as part of recent work benchmarking PSI-BLAST in genome annotation.


    Pairwise comparison of biological networks. PHUNKEE searches for similar subgraphs in pairs of metabolic and pairs of protein interaction networks.

  • PHYRE (Academic use only)

    Protein Homology/analogY Recognition Engine


    This is a Molecular Graphics package for the display of proteins and nucleic acids. PREPI is freely available to non-profit making organisations.

    Historical/Superseded Servers,Software & Databases

    Here is a link to our groups previous servers, software & databases, some of which have been superseded. Please note that these are not supported.

    Last updated 21 March 2007