CATH Documentation

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Dr Oliver Redfern

Posing on the southbank of the Thames

Post-Doctoral Research fellow

I work as part of the Midwest Consortium for Structural Genomics, aiding target selection and analysis of the novelty of the protein structures they produce. In parallel, I also develop methods for homology recognition and function prediction from protein structure and sequence.

Academic Background

  • 1998-2001 BSc(Hons) First Biochemistry, University of Warwick
  • 2001-2005 PhD Biochemistry (Computational Biology), University College London

Research Interests

My PhD was focussed on developing novel methods to enhance the speed of structure classification in the CATH database. With this aim, I developed the structure comparison method CATHEDRAL to effectively decompose whole protein structures into their component domains. I have also been involved with the analysis of large, functional diverse domain superfamilies in CATH, and as a consequence have developed a method called FLORA to discriminate between differetn functional families within these superfamilies.

Selected Publications

FLORA: a novel method to predict protein function from structure in diverse superfamilies.
Redfern OC, Dessailly BH, Dallman TJ, Sillitoe I, Orengo CA
PLoS Comput Biol5pe1000485(2009 Aug)
The CATH classification revisited--architectures reviewed and new ways to characterize structural divergence in superfamilies.
Cuff AL, Sillitoe I, Lewis T, Redfern OC, Garratt R, Thornton J, Orengo CA
Nucleic Acids Resp(2008 Nov 7)
Exploring the structure and function paradigm.
Redfern OC, Dessailly B, Orengo CA
Curr Opin Struct Biol18p394-402(2008 Jun)
CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.
Redfern OC, Harrison A, Dallman T, Pearl FM, Orengo CA
PLoS Comput Biol3pe232(2007 Nov)
Predicting protein function from sequence and structure.
Lee D, Redfern O, Orengo C
Nat Rev Mol Cell Biol8p995-1005(2007 Dec)
Structural diversity of domain superfamilies in the CATH database.
Reeves GA, Dallman TJ, Redfern OC, Akpor A, Orengo CA
J Mol Biol360p725-41(2006 Jul 14)

Other Interests

Current affairs, comedy, whiskey.

Links

http://www.cathdb.info/cgi-bin/CathedralServer.pl

Other CATH Team Members

Person Description
benoit Former Member In September 2011 I moved to Osaka, Japan, to work as a Post-Doctoral Fellow in Dr Mizuguchi's group at the National Institute of Biomedical Innovation. Research Interests My main research interests include the study of interactions between proteins and other molecules, both at the structural and network levels.
clegg [Andrew with a half-metre sausage, found (and eaten) on holiday in Germany recently] Senior Research Associate, CATH Development A member of the Orengo group since June 2008, I am the technical lead on the FuncNet platform, which brings together an ensemble of protein function analysis tools from various groups around Europe. This work is supported by the EU-funded EMBRACE and ENFIN research networks.
cuff [ Me and my Cat] CATH Manager I am responsible for the general management and manual curation of CATH. Academic Background As a undergraduate, I read for a BSc(Hons) degree in Biomedical Sciences at the University of Durham and then, after deciding I wanted to pursue Bioinformatics research, I took a MSc degree in Information Technology at the University of Teesside (this was all back in the days before MSc courses in Bioinformatics became available!).
lee [ ] Post Doctoral Research Fellow I work for the Midwest Center for Structural Genomics (MCSG). My responsibilities include selecting protein targets for structure determination, monitoring the success of target selection strategies, and providing homology models of relatives of MCSG structures.
lees Gene3D Since arriving in October 06 I've been doing development of the Gene3D database in collaboration with Corin Yeats. I also maintain the current Gene3D website. I am involved in several collaborations with experimentalists. Recently (June 2009) I have started a new post employed by ENFIN coordinating a chromosome condensation prediction project, with Juan Ranea (Malaga) and the Ellenberg group (EMBL) (amongst others). We are using novel high throughput phenotype data (Ellenberg Group) a…
lewis [Me in Malaysia] Senior Programmer I was heavily involved in the complete rewrite of the CATH update procedure that culminated in CATH v3.0.0. I am still involved in maintaining and developing CATH in an ongoing consultancy capacity. Academic Background MSc Intelligent Systems, UCL (2002-2003)
orengo See departmental staff page
perkins [Me] London Pain Consortium PhD Student I am a member of the London Pain Consortium, an initiative formed in 2002 by a grant from the Wellcome Trust. I am currently moving into the first year proper of my PhD, supervised by Christine and based in the CATH lab, having completed a year of 3 rotations, working on projects with different labs.
phil [Me] Role in CATH I am post doctoral research associate. One of my responsibilities is the target selection database for the Center for Structural Genomics of Infectious Diseases's structural genomics project. Research Interests CSGID applies state-of-the-art high-throughput structural biology technologies to experimentally characterise the three dimensional atomic structure of targeted proteins from pathogens in the NIAID Category A-C priority lists and organisms causing emerging and re-eme…
reid [Me enjoying a traditional Japanese kaiseki meal in a ryokan somewhere outside Kyoto] Me enjoying a traditional Japanese kaiseki meal in a ryokan somewhere outside Kyoto PhD student I am currently nearing the end of my PhD and planning to submit by the end of the year.
rentzsch [Me] Former PhD student I did my PhD in the lab between 2007 and 2012, funded by a EU grant (ENFIN). The ENFIN Network of Excellence aims at close collaboration between experimental and computational groups throughout Europe. I've also worked as a research assistant here.
sillitoe [Me with one of the Sillitoe clan (I'm the one on the right)] CATH Technical Manager I am responsible for the technical aspect of CATH. This generally involves maintaining and developing both the front-end interfaces (internal and external web pages and webservices) and back-end code library and databases.
studer {{ :cathteam:picture.jpg|Me}} {Role in CATH} Description of role in CATH Academic Background Current Research Interests Your research interests go here. Put some pretty pictures in with something like the following: {{ :cathteam:consensus_contact_map_example.png?300 |Example of a consensus structural alignment and contact map }}
yeats Gene3D and BioMiner Gene3D: Design and development, HMM library construction and prediction verification, and web services. Academic Background PhD at the Sanger Institute (2004), supervised by Alex Bateman (Pfam). Thesis: Biological Investigations Through Sequence Analysis.
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