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These paragraphs are not necessarily regularly updated - if you want to know what I'm planning next check the section on the left or come and talk to me (safer option)!
Complete references for the papers mentioned below can be found under the PUBLICATIONS tab.
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Protein-protein interactions- We are interested in predicting the druggability of protein-protein interactions.
The group (Paul Ashford) has developed a method for easy visualisation of conservation and variability
of surface pockets across varied ensembles of protein conformers. These have the potential to reveal
potential allosteric sites that could be targeted. This work is in collaboration
with Dr Mark Williams and Professor David Moss (BBK), and was part-funded by Pfizer.
- Reference: Ashford et al. (2011, under review).
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Protein-small molecule interactions- In the past we have applied docking methods to predict the binding mode and affinity of
small molecule ligands to proteins, in collaboration with several experimental groups. We
are also currently employing computational methods that allow the prediction and comparison
of binding pockets across related protein structures. Finally, we are currently employing
molecular dynamics simulations for the study of conformational flexibiligy and its role in
ligand binding, as well as steered molecular dynamics for the study of (un)binding of ligands.
- References: Patschull et al. (2011, under review), Patschull, Segu et al. (2011),
Chang et al. (2011), Guzman et al. (2011), Gooptu et al. (2009).
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Fragment-based approaches to the study of protein-ligand interactions- We have recently collaborated with researchers from the Istituto Italiano di Technologia on
a project that led to the creation of SERAPhiC, a high-quality
dataset of protein-fragment crystal structures from the PDB that can be used as a benchmark for
the development of new software and scoring functions for the prediction of protein-fragment
interactions.
- Reference: Favia et al. (2011).
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- We are also currently developing software for analysing the interactions between ligand fragments
and protein environments (Spiteri & Nobeli (2011), unpublished work).
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The metabolome and metabolic pathways-
- We have a long-standing interest 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.
- References: Macchiarulo et al. (2009), Bashton et al. (2009), Bashton et al. (2006),
Nobeli & Thornton (2006), Nobeli et al. (2003).
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- In collaboration with Dr Adrian Shepherd (BBK), we are exploring the reliability of homology-based
metabolic pathway reconstructions (Jan Czarnecki, PhD student). Jan is also developing text mining
software for extracting information from the literature that could be used to validate and enrich
metabolic networks. His studentship is part-funded by Unilever.
- Reference: Czarnecki et al. (2011, under review).
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- In the near future we are planning a collaboration in the area of plant metabolomics - watch this space
for details!
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Regulatory RNAs-
- We are currently interested in computational methods for predicting RNA riboswitches. The group is also
involved in structural studies of RNA-binding proteins (Anathe Patschull, PhD student under the primary
supervision of Dr Tracey Barrett).
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- In the coming months we will be building a collaboration with Dr Eugene Schuster (UCL) to study RNAs
involved in the regulation of ageing in nematode worms. This project will be available through the
scheme of MRC studentships available for 2012 entry in the department of Biological Sciences (BBK).
Details will appear soon on the departmental website.
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Interaction promiscuity of proteins-
- In the past we have been interested in the origin and mechanisms of binding and catalytic promiscuity.
We are currently attempting to construct predictive computational models of the ligand-binding promiscuity
of proteins (Krzysztof Szkop).
- References: Nobeli et al. (2009), Macchiarulo et al. (2004).
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Old and current group members (in reverse chronological order of joining)PhD students & PhD rotation students- Jan Czarnecki , BBSRC CASE PhD student (industrial sponsor: Unilever), first supervisor: Dr A. Shepherd - Text mining to facilitate metabolic pathway reconstructions.
- 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)
- WT PhD student, (2010/2013) - Computational and experimental studies of riboswitches (first supervisor: Dr Tracey Barrett)
- Paul Ashford, BBSRC CASE PhD student, BBK (2008/2011) - industrial supervisor: Dr A. Alex (Pfizer Ltd), second academic supervisor: Dr Mark Williams
- Jonathan Myles, part-time PhD student, BBK (2008 - break in study) - first supervisor: Dr A. Shepherd
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MSc/MRes students- Paul Golby, part-time MSc student, BBK (2011,2012)
- Jaytanya Rajachandrasekar, MSc student, BBK (2011) - with Dr Karen Abraham and Dr A. Shepherd
- Christian Spiteri, MSc student, BBK (2011)
- Jan Czarnecki, part-time MSc student, BBK (2010)
- Alice Povia, MSc student, BBK (2010) - Investigation of surface binding pockets among sets of homologous protein structures
- Danai Fimereli, MSc student, BBK (2010) -
- Khaleda Begum, MSc student, BBK (2010) - with Dr A. Shepherd (Design and implementation of a scientific workflow for the calculation of the probability of a protein residue to be part of a binding site)
- Rosalind Jack, MSc student, BBK (2010) - with Dr A. Shepherd and Unilever (Metabolic network reconstructions for Malassezia organisms)
- 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 )
- 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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Others- Krzysztof Szkop, Undergraduate internship student (Summer 2011) - Catalytically promiscuous proteins
- Wei Nee Lim, Undergraduate internship student (Summer 2009) - COX/LOX inhibition
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