Staff Profile:Dr Liam McGuffin

Name:

Dr Liam McGuffin

Job Title:

Academic, Harborne Bldg

Responsibilities:

Lecturer in Bioinformatics; Admissions Tutor for Biological Sciences

Areas of Interest:

Research Interests:

One of the fundamental areas of study in biomedical sciences is determining how proteins function within cells and how that function translates to health. To deliver on the promise of next generation sequencing for health care and personalised medicine, we must understand the information implicit in the genome, specifically, the functions of the proteins that are encoded by the genes.  Individual protein chains fold into specific three dimensional structures and bind with one another to form complexes that perform essential functions. The 3D fold of a protein is therefore key to the cell functioning correctly and protein misfolding is a direct cause of disease - Alzheimer's, Parkinson's and CJD being well known, if extreme, examples.

Determining the 3D fold of a protein is not always straight forward. In cases where the structure of a protein has been determined experimentally, the fold can then be directly visualised. However, solving structures experimentally is time consuming and expensive and so the vast majority of proteins with known sequences have unknown structures. Fortunately, in the majority of cases we can use predictive tools that allow us to rapidly and accurately model the shapes of proteins in silico, which helps us to determine their likely functions and interactions.

My main interest is in the development of computational methods for rapidly and confidently predicting the structures, functions and interactions of proteins using only amino acid sequence information. Once a catalogue of accurately predicted structures for the majority of proteins within a cell is available, the aim is to predict their ability to interact with small molecules and each other, to form the complex cellular machinery upon which life depends. This vital information will allow us to produce novel or more efficient products for use in medicine and will help us to better understand the mechanisms of the leading causes of death, such as heart disease and stroke.

My novel bioinformatics tools for predicting protein structures and functions rank among the top few internationally. The DISOclust, ModFOLD and FunFOLD methods and the IntFOLD integrated server for the prediction of structures and ligand interactions, have been particularly successful at the recent CASP competitions - further details can be seen on my group homepages: http://www.reading.ac.uk/bioinf/

Complete List of Publications

Google Scholar Profile with Citation Indices

Research groups / Centres:

Molecular and Cellular Medicine group

Institute for Cardiovascular & Metabolic Research (ICMR) 

Publications:

Y

Jump to: 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000

Number of items: 38.

2013

• McGuffin, L. J., Buenavista, M. T. and Roche, D. B. (2013) The ModFOLD4 server for the quality assessment of 3D protein models. Nucleic Acids Research. ISSN 1362-4962 doi: 10.1093/nar/gkt294

2012

• Pedersen, C., van Themaat, E. V., McGuffin, L., Abbott, J. C., Burgis, T. A., Barton, G., Bindschedler, L. V., Lu, X., Maekawa, T., Weßling, R., Cramer, R., Thordal-Christensen, H., Panstruga, R. and Spanu, P. D. (2012) Structure and evolution of barley powdery mildew effector candidates. BMC Genomics, 13 (1). p. 694. ISSN 1471-2164 doi: 10.1186/1471-2164-13-694
• Roche, D. B., Buenavista, M. T. and McGuffin, L. (2012) Predicting protein structures and structural annotation of proteomes. In: Roberts, G. (ed.) Encylopedia of Biophysics. Springer-Verlag , Berlin Heidelberg . ISBN 9783642167119 (In Press)
• Roche, D. B., Buenavista, M. T. and McGuffin, L. J. (2012) FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions. PLoS ONE, 7 (5). e38219. ISSN 1932-6203 doi: 10.1371/journal.pone.0038219
• Buenavista, M. T., Roche, D. B. and McGuffin, L. J. (2012) Improvement of 3D protein models using multiple templates guided by single-template model quality assessment. Bioinformatics, 28 (14). pp. 1851-1857. ISSN 1460-2059 doi: 10.1093/bioinformatics/bts292
• Fuller, S. J., McGuffin, L. J., Marshall, A. K., Giraldo, A., Pikkarainen, S., Clerk, A. and Sugden, P. (2012) A novel, non-canonical mechanism of regulation of MST3 (mammalian Sterile20-related kinase 3). Biochemical Journal, 442 (3). pp. 595-610. ISSN 0264-6021 doi: 10.1042/BJ20112000

2011

• Bindschedler, L. V., McGuffin, L. J., Burgis, T. A., Spanu, P. D. and Cramer, R. (2011) Proteogenomics and in silico structural and functional annotation of the barley powdery mildew Blumeria graminis f. sp. hordei. Methods, 54 (4). pp. 432-441. ISSN 1046-2023 doi: 10.1016/j.ymeth.2011.03.006
• Roche, D. B., Buenavista, M. T., Tetchner, S. J. and McGuffin, L. J. (2011) The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction. Nucleic Acids Research, 39 (Web Server issue). W171-W176. ISSN 1362-4962 doi: 10.1093/nar/gkr184
• McGuffin, L. J. and Roche, D. B. (2011) Automated tertiary structure prediction with accurate local model quality assessment using the IntFOLD-TS method. Proteins: Structure, Function, and Bioinformatics, 79 (S10). pp. 137-146. ISSN 1097-0134 doi: 10.1002/prot.23120
• Roche, D. B., Tetchner, S. J. and McGuffin, L. J. (2011) FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. BMC Bioinformatics, 12 (1). p. 160. ISSN 1471-2105 doi: 10.1186/1471-2105-12-160

2010

• McGuffin, L. J. (2010) Model quality prediction. In: Rangwala, H. and Karypis, G. (eds.) Introduction to protein structure prediction: methods and algorithms. Wiley, pp. 323-342. ISBN 9780470470596
• Roche, D. B., Tetchner, S. J. and McGuffin, L. J. (2010) The binding site distance test score: a robust method for the assessment of predicted protein binding sites. Bioinformatics, 26 (22). pp. 2920-2921. ISSN 1460-2059 doi: 10.1093/bioinformatics/btq543
• McGuffin, L. J. and Roche, D. B. (2010) Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics, 26 (2). pp. 182-188. ISSN 1460-2059 doi: 10.1093/bioinformatics/btp629

2009

• McGuffin, L. J. (2009) Insertions and deletions, their molecular mechanisms and their impact on sequence alignments. In: Rosenberg, M. S. (ed.) Sequence Alignment: Methods, Models, Concepts, and Strategies. University of California Press, pp. 23-38. ISBN 9780520256972
• McGuffin, L. J. (2009) Prediction of global and local model quality in CASP8 using the ModFOLD server. Proteins-Structure Function and Bioinformatics, 77. pp. 185-190. ISSN 0887-3585 doi: 10.1002/prot.22491
• Marsden, R. L., McGuffin, L. J. and Jones, D. T. (2009) Rapid protein domain assignment from amino acid sequence using predicted secondary structure. Protein Science, 11 (12). pp. 2814-2824. ISSN 09618368 doi: 10.1110/ps.0209902

2008

• McGuffin, L. J. (2008) Aligning sequences to structures. Methods in Molecular Biology, 413. pp. 61-90. ISSN 1064-3745
• McGuffin, L. J. (2008) Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. Bioinformatics, 24 (16). pp. 1798-1804. ISSN 1367-4803 doi: 10.1093/bioinformatics/btn326
• McGuffin, L. J. (2008) The ModFOLD server for the quality assessment of protein structural models. Bioinformatics, 24 (4). pp. 586-587. ISSN 1367-4803 doi: 10.1093/bioinformatics/btn014
• McGuffin, L.J. (2008) Protein fold recognition and threading. In: Computational Structural Biology. World Scientific Publishing Ltd, pp. 37-60. ISBN 9789812778772

2007

• McGuffin, L. J. (2007) Benchmarking consensus model quality assessment for protein fold recognition. Bmc Bioinformatics, 8. p. 15. ISSN 1471-2105 doi: 10.1186/1471-2105-8-345

2006

• McGuffin, L. J., Smith, R. T., Bryson, K., Sorensen, S. A. and Jones, D. T. (2006) High throughput profile-profile based fold recognition for the entire human proteome. BMC Bioinformatics, 7. p. 288. ISSN 1471-2105 doi: 10.1186/1471-2105-7-288

2005

• Jones, D. T., Bryson, K., Coleman, A., McGuffin, L. J., Sadowski, M. I., Sodhi, J. S. and Ward, J. J. (2005) Prediction of novel and analogous folds using fragment assembly and fold recognition. Proteins: Structure, Function, and Bioinformatics, 61 (S7). pp. 143-151. ISSN 1097-0134 doi: 10.1002/prot.20731
• Pettitt, C. S., McGuffin, L. J. and Jones, D. T. (2005) Improving sequence-based fold recognition by using 3D model quality assessment. Bioinformatics, 21 (17). pp. 3509-3515. ISSN 1460-2059 doi: 10.1093/bioinformatics/bti540
• Bryson, K., McGuffin, L. J., Marsden, R. L., Ward, J. J., Sodhi, J. S. and Jones, D. T. (2005) Protein structure prediction servers at University College London. Nucleic Acids Research, 33 (S2). W36-W38. ISSN 1362-4962 doi: 10.1093/nar/gki410

2004

• Sodhi, J. S., McGuffin, L. J., Bryson, K., Ward, J. J., Wernisch, L. and Jones, D. T. (2004) Automatic prediction of functional site regions in low-resolution protein structures. In: Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004. IEEE, pp. 702-703. doi: 10.1109/CSB.2004.1332551
• Ward, J. J., McGuffin, L. J., Bryson, K., Buxton, B. F. and Jones, D. T. (2004) The DISOPRED server for the prediction of protein disorder. Bioinformatics, 20 (13). pp. 2138-2139. ISSN 1460-2059 doi: 10.1093/bioinformatics/bth195
• McGuffin, L. J., Street, S., Sorensen, S.-A. and Jones, D. T. (2004) The Genomic Threading Database. Bioinformatics, 20 (1). pp. 131-132. ISSN 1460-2059 doi: 10.1093/bioinformatics/btg387
• McGuffin, L. J., Street, S. A. , Bryson, K. , Sørensen, S.‐A. and Jones, D. T. (2004) The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms. Nucleic Acids Research, 32 (S1). D196-D199. ISSN 1362-4962 doi: 10.1093/nar/gkh043
• Sodhi, J. S., Bryson, K., McGuffin, L. J., Ward, J. J., Wernisch, L. and Jones, D. T. (2004) Predicting metal-binding site residues in low-resolution structural models. Journal of Molecular Biology, 342 (1). pp. 307-320. ISSN 0022-2836 doi: 10.1016/j.jmb.2004.07.019
• Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F. and Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the Three Kingdoms of Life. Journal of Molecular Biology, 337 (3). pp. 635-645. ISSN 0022-2836 doi: 10.1016/j.jmb.2004.02.002

2003

• Jones, D. T. and McGuffin, L. J. (2003) Assembling novel protein folds from super-secondary structural fragments. Proteins: Structure, Function, and Genetics, 53 (S6). pp. 480-485. ISSN 0887-3585 doi: 10.1002/prot.10542
• McGuffin, L. J. and Jones, D. T. (2003) Benchmarking secondary structure prediction for fold recognition. Proteins: Structure, Function, and Genetics, 52 (2). pp. 166-175. ISSN 0887-3585 doi: 10.1002/prot.10408
• McGuffin, L. J. and Jones, D. T. (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics, 19 (7). pp. 874-881. ISSN 1460-2059 doi: 10.1093/bioinformatics/btg097
• Ward, J. J., McGuffin, L. J., Buxton, B. F. and Jones, D. T. (2003) Secondary structure prediction with support vector machines. Bioinformatics, 19 (13). pp. 1650-1655. ISSN 1460-2059 doi: 10.1093/bioinformatics/btg223

2002

• McGuffin, L. J. and Jones, D. T. (2002) Targeting novel folds for structural genomics. Proteins: Structure, Function, and Bioinformatics, 48 (1). pp. 44-52. ISSN 1097-0134 doi: 10.1002/prot.10129

2001

• McGuffin, L. J., Bryson, K. and Jones, D. T. (2001) What are the baselines for protein fold recognition? Bioinformatics, 17 (1). pp. 63-72. ISSN 1460-2059 doi: 10.1093/bioinformatics/17.1.63

2000

• McGuffin, L. J., Bryson, K. and Jones, D. T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16 (4). pp. 404-405. ISSN 1460-2059 doi: 10.1093/bioinformatics/16.4.404

This list was generated on Wed Jun 19 14:33:09 2013 BST.