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Structural Bioinformatics

Sternberg lab Imperial college

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.


3DLigandSite

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.


3D-PSSM (Academic use only)

Please note that 3DPSSM has been superseded by PHYRE.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.


CombFunc

Protein function prediction server


MC-TopLog (Multi-Clause TopLog)

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.


PHYRE2 (Academic use only)

Protein Homology/analogY Recognition Engine.

PINALOG (Academic use only)

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.

 

PDB tools

RasMol 2.6 beta-1a

MDL Chime

WebLab Viewer 2.01

Swiss PDBViewer/DeepView

Drug repurposing

LINKS L100 - http://www.lincscloud.org/