I have moved to the University of Kent
I can still be contacted at mark.wass04 AT imperial.ac.uk or new email address m.n.wass AT kent.ac.uk.
Prediction of Protein-Protein interactions using protein docking
Working with Alfonso Valencia at the CNIO in Madrid we have demonstrated the ability to use a protein docking method to predict protein interaction partners (pairs of proteins that interact). Protein docking programs are generally used to predict the shape of the complex formed between pairs of proteins that are known to interact. This is a difficult problem and docking methods often fail to generate accurate models of complexes. It had therefore been widely thought that it was beyond the scope of such program to predict IF two proteins interact.
For a set of known complexes we demonstrated that it is possible to distinguish the docking scores of the real complex from the individual proteins docked with a large set of decoy proteins. For more details see Wass et al., 2011, Mol Syst Biol 7:469.
Prediction of Ligand binding sites
My work on predicting ligand binding sites started when we participated in CASP8. We made manual predictions of ligand binding sites by identifying homologous structures and superimposing them on models of the predicted structure of the target protein. This effectively superimposed the ligands of the homologues onto the model of the target protein from which we predicted the binding site of the target protein. More details are available on our CASP results page and our paper in the CASP8 Special Issue of Proteins - Wass, M.N. and Sternberg, M.J. (2009) Prediction of ligand binding sites using homologous structures and conservation at CASP8.Proteins, 77 Suppl 9:147-51. PubMed. We have continued to perform well in the recent CASP9 assessment.
After CASP8 we automated our manual predictive approach in the 3DLigandSite server (http://www.sbg.bio.ic.ac.uk/3dligandsite).
ConFunc - Protein Function Prediction
Convergent Evolution of Enzyme active sites
David, A., Razali, R., Wass, M.N.*, Sternberg, M.J.E.* (2011) Protein-protein interaction sites are hot spots for disease-associated non-synonymous SNPs. Human Mutation, In press.
Chambers JC, Zhang W, Sehmi J, Li X, Wass M.N.* et al., (2011) Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma. Nat Genet. doi: 10.1038/ng.970 Pubmed
Wass M.N., David A., Sternberg M.J. (2011) Challenges for the prediction of macromolecular interactions. Curr Op Struct Biol. 21:382-90 Pubmed
Wass M.N., Fuentes G., Pons, C., Pazos F., Valencia A. (2011) Towards the prediction of interaction partners using Physical docking. Mol Syst Biol 7:469 Pubmed
Sinden R.E., Talman A., Marques S.R., Wass M.N., Sternberg M.J. (2010) The flagellum in malarial parasites. Curr Opin Microbiol. 13:491-500 PubMed
Wass M.N, Kelley L.A. and Sternberg M.J. (2010) 3DLigandSite: predicting ligand-binding sites using similar structures.NAR 38, W469-73 PubMed
Chambers J.C. et al., (2010) Genetic loci influencing kidney function and chronic kidney disease. Nat Genet 42:373-5 PubMed
Chambers, J.C. et al., (2010) Genetic variation in SCN10A influences cardiac conduction. Nat Genet, 42:149-52 PubMed
Chambers, J.C., Zhang, W., Li, Y., Sehmi, J., Wass, M.N. et al., (2009) Genome-wide association study identifies variants in TMPRSS6 associated with hemoglobin levels. Nat Genet, 41, 1170-2. PubMed
Wass, M.N. and Sternberg, M.J. (2009) Prediction of ligand binding sites using homologous structures and conservation at CASP8. Proteins, 77 Suppl 9:147-51. PubMed
Wass, M.N. and Sternberg, M.J. (2008) ConFunc--functional annotation in the twilight zone, Bioinformatics, 24, 798-806. PubMed
Gherardini, P.F., Wass, M.N., Helmer-Citterich, M. and Sternberg, M.J. (2007) Convergent Evolution of Enzyme Active Sites Is not a Rare Phenomenon, J Mol Biol, 372, 817-845. PubMed
Brand, M. D., Boutilier, R. G., Wass, M., St-Pierre, J. & Bishop, T. (2001). Mitochondrial proton leak in metabolic depression. In Molecular Mechanisms of Metabolic Arrest: Life in Limbo, edited by K. B. Storey, 59-76
3DLigandSite: Predicting ligand binding sites using similar structures. AFP SIG 2011, Vienna, Austria.
Towards the prediction of interaction partners using Physical docking. ISMB 2010, Boston, USA.
Towards the prediction of interaction partners using Physical docking. 3D-SIG 2010, Boston USA.
Protein Modelling - structure, function and interactions. Brains of Britain, UK Biotechnology Showcase at AusBiotech, Melbourne, Australia, October 2009
Using function, conservation and structure to predict ligand binding sites. CASP 8 Sardinia, December 2008
ConFunc – functional annotation in the twilight zone. CASP7.5, Madrid, Spain, April 2008
ConFunc: Feature derived profiles for functional annotation. AFP SIG, Vienna, Austria, July 2007.
Email: m.wass04 AT imperial.ac.uk OR m.n.wass AT kent.ac.uk