Servers, Software & Databases

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

3D-GARDEN 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. PHUNKEE 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 PREPI 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 Historical/Superseded Servers,Software & Databases Here is a link to our groups previous servers, software & databases, some of which have been superseded.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