Protein

David Jones - Bioinformatics Group, Dept. of Computer Science, UCL

Prof. Jones's principal research interests are in protein structure prediction and analysis and simulations of protein folding. Under direction from Prof. Jones, the Bioinformatics Group's main aim is to develop and apply state-of-the-art mathematical and computer science techniques to problems now arising in the life sciences.

Databases: Genome Threading Database (GTD)
Tools: Threader, GenThreader, pGenThreader, MEMSAT, PSIPRED, DisoPred
URL: Bioinformatics Group

Christine Orengo - BSM group, Dept. of Biochemistry, UCL

Prof. Orengo's research chiefly concerns the development of algorithms for the classification of domain and protein families, the main products of this research being the CATH and Gene3D databases. Her group is also involved in designing methods to identify sequence or structural features associated with specific functional properties, with the ultimate goal of being able to predict the possible function of any gene sequence assigned to one of the protein families in the database.

Databases: CATH, DHS, Gene3D
Tools: SSAP, GRATH, Impala
URL: Homepage

Andrew Martin - BSM group, Dept. of Biochemistry, UCL

Dr. Martin is best known for his work on analysis and modelling of antibodies and analysis of the effects of mutations on protein structure and function. His group is analysing antibody sequence and structure with a view to understanding how the immune system tailors binding to a given antigen and how antibodies can be humanised or sythesised. Initial studies of the effects of mutations concentrated on the tumour suppressor protein p53, but now looks at all proteins for which mutation data are available. Protocols for the analysis of the structural and functional consequences of single amino acid mutations are being enhanced with a view to using them predictively. Other work in the group has looked at improving sequence alignment for protein modelling and creating automated pipelines for protein sequence annotation.

Databases: SAAP, OMIM Missense Mutations Database, PDBSWS, KabatMan (Antibody Analysis), PDBSprotEC, Orthofind
Tools: ProFit, APAT, AVP, CheckHBond
URL: Homepage

Marketa Zvelebil - Breakthrough Breast Cancer Research Centre, Institute of Cancer Research

Dr. Zvelebil's research relating to protein structure concerns the modelling of large multidomain proteins, such as PI-3 Kinase family. Producing such models is vital for the precise understanding of ligand specificity and therefore drug analysis and design. Recent work with a variety of internal and external collaborators has produced models for class I and II PI-3 kinases which can be used for detailed investigations of a large set of ligands by both manual and automatic methods. Other modelling interests include the ASPP-family of proteins in complex with p53/p65 and p73 and various serine racemases. Dr Zvelebil's group is also involved in systems biology research of signalling pathways concerned with migration and inflammation, as well as writing automated procedures for systems biology online.

Databases: LIBRA
URL: Homepage

Steve Perkins - BSM group, Dept. of Biochemistry, UCL

Prof. Perkins is best known for his protein solution structural studies of antibodies and complement, side-by-side with the database analysis of the effects of mutations on the coagulation and complement of proteins. He has developed websites that bring together phenotypic and structural information on complement factor H (associated with age-related macular degeneration and renal failure) and coagulation Factor XI (associated with bleeding disorders).

Databases: Factor H, Factor XI
URL: Homepage

Maya Topf - Lecturer in Bioinformatics, Crystallography, Birkbeck

Development and application of methods in computational structural biology to study the structure and function of macromolecular assemblies. The methods are used in conjunction with experimental methods in particular cryo-electron microsocopy.

URL: Homepage

Mark Williams - Lecturer in Bioinformatics, Crystallography, Birkbeck

Dr Williams' research is concerned with understanding the structural and physical principles of biomolecular complex formation and how those principles control the behaviour of heterogeneous populations of complexes in functional biological systems. A wide variety of computational approaches are used by the group to complement and interpret experimental data. The group are engaged in the development of databases and structural analysis tools to enable investigation of correlations between structure and the thermodynamics of molecular interactions, in trying to improve the quality of tools for protein structure determination, and in the creation and application of software for the stochastic simulation of biological systems from the atomic to the cellular level.

Databases: SCORPIO
Tools: Pro_ACT
URL: Homepage

Irilenia Nobeli - Lecturer in Bioinformatics, Crystallography, Birkbeck

Development and application of bioinformatics and chemoinformatics methods to analyse and compare endogenous and exogenous metabolites, understand and predict molecular recognition, and predict protein function.

URL: Homepage

Denise Gorse - Lecturer in Bioinformatics, Computer Science, UCL

Dr. Gorse's research focuses on how proteins find their correct 3-dimensional structures upon folding. She uses a combination of neural network algorithms and other mathematical techniques - for example Fourier and wavelet transformation methods, and the application of background fields that simulate the action of chaperonin systems in the cell - to try to predict how proteins fold and how they associate into more complex multimeric molecules.

URL: Homepage

Bonnie Wallace - Crystallography, Birkbeck

Prof Wallace's research incorporates Bioinformatics studies with experimental research in Structural Biology and Biophysics. Her research falls in two general areas: Studies on the structure and function of Voltage-Gated Sodium Channels, which includes molecular modelling and ligand docking studies as the basis for rational drug design, and methods development for Circular Dichroism spectroscopy, which includes the development of the popular Dichroweb secondary structure analysis website, the creation of the CDtoools software for spectral processing, analysis and archiving, and the development of the Protein Circular Dichroism Data Bank (PCDDB), a deposition and searchable archives of macromolecular circular dichroism spectra and metadata.

Database: PCDDB
URL: Homepage