Tools - Available Servers, Software & Databases

Much of our research is disseminated in the form of publicly available software, databases and web based servers. This page contains a list of our currently available tools as well as a list of previous works.

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:

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Please note that 3DPSSM has been superseded by PHYRE.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

SuSPect

A server for predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms (nsSNPs). By integrating sequence, structural and systems biology-based features, SuSPect predicts how likely an nsSNP is to cause disease and gives an explanation of how it may have its effects.

WIBL

The Workbench for Integrative Systems Biology is a portal-based workbench for interdisciplinary systems biology projects. For further information about WIBL please click here.

WINARNS

Server for global alignment of protein-protein interaction networks

Previous/Superseded works (only partially supported)

Here is a list of our groups previous servers, software & databases, some of which have been superseded. Please note that these are listed here for historical purposes and only partially supported.

PREPI

This is a Molecular Graphics package for the display of proteins and nucleic acids. PREPI can display many different types of molecular representions including cartoons and molecular surface. PREPI is freely available to non-profit making organisations.

3D-DOCK

Predictive protein-protein docking.
• FTDOCK performs rigid-body docking on two biomolecules in order to predict their correct binding geometry based on surface shape complementarity and electrostatic interactions.

• RPSCORE reranks candidate docking orientations produced by FTDOCK using an empirical scoring function derived from a library of protein-protein interfaces.

• MULTIDOCK (Academic use only - Commerical license available) provides a method for refining the interface between two proteins at the atomic level given an initial docked complex (such as one generated by FTDOCK).

3D-GENOMICS (Academic use only)

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

3D-JIGSAW

Homology modelling server. This is being hosted & developed by the Cancer Research U.K.

BioBiblioMetrics

Information retrieval and visualization from co-occurrences of yeast gene names in Medline abstracts. This is being hosted by Cancer Research U.K.

Domains

Users may compute domain assignments for their own coordinate data using the DAD algorithm.

Genome Assignments

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

Heavy Atom Databank

This databank contains details of experimental conditions used for protein crystallization, including details on compounds, pH ranges etc. There is also structural information on the binding sites (protein environment in crystal and solvent) of heavy atoms (e.g. HG, PT, U).

ILP

Inductive Logic Programming - Machine-learning techniques applied to learning principles of protein structure, predicting structurally conserved secondary structure elements and predicting which parts of a structure form during the early stages of folding.This databank contains details of experimental conditions used for protein crystallization,

Loop Database

This databank contains conformational clusters and consensus sequences for protein loops that have been derived by computational analysis of their structures in a non-redundant set of 233 proteins with less than 25% sequence homology (X-ray resolution better than 2.5 A). This is being hosted & developed by the Cancer Research U.K.

PHUNKEE

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

PRED-GUIDE

Guide to predicting protein 3D structure (1999).

SAWTED

PSI-BLAST server with validation of borderline hits using quantitative assessment of database annotation similarities. This is being hosted by the Cancer Research U.K.