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.
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
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 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Please note that 3DPSSM has been superseded by PHYRE.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.
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
PHYRE2 (Academic use only)
Protein Homology/analogY Recognition Engine.
PINALOG (Academic use only)
Alignment of Interactomes
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.
The Workbench for Integrative Systems Biology is a portal-based workbench for
interdisciplinary systems biology projects. For further information about WIBL please click here.
Server for global alignment of protein-protein interaction networks
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which have been superseded.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.
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
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).
A database for protein structure and function annotation across different
Homology modelling server. This is being hosted & developed by the Cancer Research U.K.
Information retrieval and visualization from co-occurrences of yeast gene
names in Medline abstracts. This is being hosted by Cancer Research U.K.
Users may compute domain assignments for their own coordinate data
using the DAD algorithm.
Structural assignments for the Mycoplasma genitalium and
Mycobacterium tuberculosis genomes as part of recent work
benchmarking PSI-BLAST in genome annotation.
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).
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,
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.
Pairwise comparison of biological networks. PHUNKEE searches for similar subgraphs in pairs of
metabolic and pairs of protein interaction networks.
Guide to predicting protein 3D structure (1999).
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.