- About BIORISE
Sternberg lab Imperial college
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.
3DLigandSite predicts ligand binding sites using ligand binding data from homologous structures. Users can either input a sequence, or a protein structure. Where a sequence is used, Phyre, our in-house structure prediction server first models the protein structure.
Please note that 3DPSSM has been superseded by PHYRE. Protein fold recognition using 1D and 3D sequence profiles coupled with secondary structure and solvation potential information.
Protein function prediction server
An integrative logic-based machine learning approach, which implements an abductive ILP (A/ILP) framework to hypothesise regulatory reactions that underlie metabolic modulations. Download the MC-TopLog.tar.gz (69MB) file here.
Protein Homology/analogY Recognition Engine.
Alignment of Interactomes
Thorton lab EMBL-EBI
MACiE- Annotated enzyme reaction mechanisms.
PDBsum- Structural analysis, including PROCHECK, for user-submitted PDB file.
PoreLogo- Visualization of sequence and conservation of pore-lining residues in transmembrane protein structures.
PoreWalker- Detection and characterisation of transmembrane protein channels.
ProFunc- Protein function prediction from protein 3D structure.
SAS- Sequence Annotated by Structure.
LINKS L100 - http://www.lincscloud.org/