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The metabolome-
- We are interested in the analysis of the collections of endogenous metabolites in model organisms from a structural and physicochemical point of view. We use chemoinformatics methods to reveal the relationships between metabolites within a species, compare metabolites from different species, and finally compare endogenous metabolites to exogenous (human made or environmental) small molecules. We are also interested in localisation information for endogenous and exogenous metabolites.
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Small molecule - macromolecule interactions-
- In the past we have studied various aspects of protein-ligand interactions, including the building and testing of model potentials, aspects of molecular recognition, and docking as an aid in identifying protein function. Currently our interests concentrate on mapping endogenous metabolites to protein domains using information from the Protein Data Bank, protein function prediction using docking, protein-ligand interactions studied with information theory, and small molecule -RNA interactions.
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Specificity vs promiscuity-
- We are interested in discovering the extent of promiscuity in protein-ligand interactions. There are two approaches we concentrate on: a) using molecular docking to provide leads for promiscuity and hence to narrow down the range of proteins and small molecules that experimentalists need to test and b) using text mining to retrieve evidence of promiscuity from the literature.
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Metabolic pathways-
- We are primarily interested in projecting human metabolic pathways on the space defined by the structures of the metabolites comprising them, i.e. a metabolite-centric view of reaction networks. This novel view allows us to understand possible cross-reactivity and dependencies between pathways, and has the potential to help us explain the side effects of enzyme-targeting drugs.
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Enzymatic reaction prediction-
- Using computational methods it is possible to narrow down the number of enzymatic reactions a molecule can undergo in theory. This, in combination with other approaches, such as docking, can help us predict the possible metabolic routes available to a small molecule inside an organism.
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Old and current group members (in reverse chronological order of joining)-
- Anna Heddell, WT rotation PhD student (winter/spring 2010) - Computational screening for inhibitors of the tuberculosis resuscitation factors (with Prof. Nick Keep)
- Anathe Patschull, WT rotation PhD student (autumn 2009) -
Computational docking of small molecules to α1-antitrysin (with Dr Bibek Gooptu)
- Niyi Atose, part-time PhD student, BBK (2009/?) - Engineering new metal binding sites on proteins
- Wei Nee Lim, Undergraduate internship student (Summer 2009) - COX/LOX inhibition
- Paul Ashford, PhD student, BBK (2008/2011) - industrial supervisor: Dr A. Alex (Pfizer Ltd), second academic supervisor: Prof. David Moss
- Jonathan Myles, part-time PhD student, BBK (2008 - break in study) - first supervisor: Dr A. Shepherd
- Jonathan Hurwitz, part-time MSc student, BBK (2008/2009)- first supervisor: Dr A. Shepherd (life in extreme environments)
- Michael Fox, MRes student, BBK (2007) - with Dr A. Shepherd (QSAR)
- Dimitris Mekras, MSc student, BBK (2006) - with Dr A. Shepherd (Metabolome 3d)
- Fatai Ogunlayi, MSc student, BBK (2006) - with Dr A. Shepherd (Text mining for protein functions)
- Ling Zhu, MRes student, York (2006) - Comparison of cognate and cognate-like ligand interactions in the PDB
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