David Lee

David 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.

Academic Background

1985 BSc in Biochemistry at UCL

1988 Fellowship of the Institute of Medical Laboratory Science (Virology) at NESCOT while working at the Royal Free Hospital

1995 Part-time MSc in Computer Modelling of Molecular and Biological Processes at Birkbeck (Distinction)

1999 PhD with Julia Goodfellow at Birkbeck

For my PhD I used various computational approaches to model the conformational change in transferrin that accompanies release of iron in response to a reduction in pH.

After hypothesizing a mechanism of action I succeeded in simulating a small conformational change using molecular dynamics. This exhibited some of the correct features; in particular there was a hinge axis between the two halfs of the domain and it almost intersected with the crystallographic hinge axis.

Current Research Interests

Protein function prediction. I am pursuing an approach to target selection in structural genomics that targets representatives of the functional diversity of protein domain sequences predicted to belong to large structural superfamilies.

Selected Publications

Predicting protein function from sequence and structure.
Lee D, Redfern O, Orengo C
Nat Rev Mol Cell Biol8p995-1005(2007 Dec)

Exploiting protein structure data to explore the evolution of protein function and biological complexity.
Marsden RL, Ranea JA, Sillero A, Redfern O, Yeats C, Maibaum M, Lee D, Addou S, Reeves GA, Dallman TJ, Orengo CA
Philos Trans R Soc Lond B Biol Sci361p425-40(2006 Mar 29)

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.
Marsden RL, Lee D, Maibaum M, Yeats C, Orengo CA
Nucleic Acids Res34p1066-80(2006)

Gene3D: modelling protein structure, function and evolution.
Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA
Nucleic Acids Res34pD281-4(2006 Jan 1)

Identification and distribution of protein families in 120 completed genomes using Gene3D.
Lee D, Grant A, Marsden RL, Orengo C
Proteins59p603-15(2005 May 15)

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.
Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C
Nucleic Acids Res33pD247-51(2005 Jan 1)

Progress towards mapping the universe of protein folds.
Grant A, Lee D, Orengo C
Genome Biol5p107(2004)

EyeSite: a semi-automated database of protein families in the eye.
Lee DA, Fefeu S, Edo-Ukeh AA, Orengo CA, Slingsby C
Nucleic Acids Res32pD148-52(2004 Jan 1)

Trimethylaminuria and a human FMO3 mutation database.
Hernandez D, Addou S, Lee D, Orengo C, Shephard EA, Phillips IR
Hum Mutat22p209-13(2003 Sep)

A structural perspective on genome evolution.
Lee D, Grant A, Buchan D, Orengo C
Curr Opin Struct Biol13p359-69(2003 Jun)

Gene3D: structural assignments for the biologist and bioinformaticist alike.
Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA
Nucleic Acids Res31p469-73(2003 Jan 1)

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.
Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA
Genome Res12p503-14(2002 Mar)

The CATH extended protein-family database: providing structural annotations for genome sequences.
Pearl FM, Lee D, Bray JE, Buchan DW, Shepherd AJ, Orengo CA
Protein Sci11p233-44(2002 Feb)

The CATH protein family database: a resource for structural and functional annotation of genomes.
Orengo CA, Bray JE, Buchan DW, Harrison A, Lee D, Pearl FM, Sillitoe I, Todd AE, Thornton JM
Proteomics2p11-21(2002 Jan)

A rapid classification protocol for the CATH Domain Database to support structural genomics.
Pearl FM, Martin N, Bray JE, Buchan DW, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA
Nucleic Acids Res29p223-7(2001 Jan 1)

VIDA: a virus database system for the organization of animal virus genome open reading frames.
Albà MM, Lee D, Pearl FM, Shepherd AJ, Martin N, Orengo CA, Kellam P
Nucleic Acids Res29p133-6(2001 Jan 1)

Assigning genomic sequences to CATH.
Pearl FM, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA
Nucleic Acids Res28p277-82(2000 Jan 1)

Other Interests

Most of my free time is spent helping out my partner with her horse.

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!).
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…
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.
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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