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Current projects (last update 24/07/04)

  • Ian Lenane (PhD student)
       Multiple time stepping and stochastic Hamiltonians in molecular simulations

  • Ben Gladwin (PhD student)
       Hamiltonian path integral simulations for large (bio)-molecular systems

  • Dmitri Mouradov (PhD student)
       Readily available distance constraints from chemical crosslinking and mass
       spectrometry experiments for high-throughput proteomics:
       Experimental implementation and feasability assessment.

  • Geoff Faulkner (Honours SS04)
       Computational rationalisation of protein crystallisation

  • Ari Craven (Honours WS04)
       Analyses of protein-protein interactions using chemical crosslinking and mass

  • Bryce Shepherd (Honours WS04)
       Assignment of genomic fragments in microbial community shotgun sequencing

  • Natalie Conners (Honours WS04)
       Identification of protein properties that affect high-throughput protein expression

  • Christophe Schmitz (exchange student from Institut des Sciences et Technique des Yvelines, Versailles France)
       Fast assignments of 15N-HSQC spectra of proteins by paramagnetic labelling

  • Open projects (last update 24/07/04)

  • Structure prediction for mammalian proteins
       with: UQ StrGx
       aim: computational support for the selection and structure determination of proteins in the UQ mouse StrGx programme

  • Rational protein crystallisation guided by light scattering and bio-physical calculations
       with: B. Kobe, Biochemistry
       aim: higher crystallisation success rate using directed experiments

  • Whole genome microbial evolution
       with: P. Hugenholtz, JGI Berkeley
       aim: marker sequence independent and more complete picture of microbial evolution

  • Protein structure refinement using paramagnetic NMR data
       with: G. Otting, ANU
       aim: more accurate NMR structures using additional long-range paramagnetic NMR restraints

  • ...and a smorgasbord of other projects

  • Older projects partly still open

  • Protein structure prediction using incomplete structural data and fragment assembly approaches.
    Despite a several decades of research, protein structure prediction from only sequence information remains a difficult task which more often fails then actually succeeds. Readily available structural information can greatly improve the success rates of prediction but are notoriously hard to implement in prediciton methods. This project will explore the approach of combining protein fragment assembly with a small number of structural constraints from experiment to generate reasonable models of protein structures.

  • Development of optimal protein score functions for ab initio protein folding of small disulfide-rich proteins.
    There are now a plethera of protein scoring functions (or force fields) for protein structure modelling. While there are often optimised to work best in particular problem domains (such as fold recognition, protein stability analysis, &c.) their performance generally breaks down when taken out of their domain. In this project a protein force field will be developed specifically for folding and refining the structure of small disulfide-rich proteins, a class of proteins where conventional force fields tend to perform particular poorly.

  • Sequence-to-structure alignment by parallel tempering.
    Sequence-sequence alignment is a well established method that enjoys high popularity with experimental and theoretical biologists. Sequence-structure alignment on the contrary is still in a very inmature state and has lots of space for improvement. This project will apply parallel tempering, global optimisation to find optimal seuqence-structure alignments for force field functions of arbitrary forms.

  • Fast searches of peptide mass fingerprints in sequence databases.
    Its low sensitivity and high accuracy makes mass spectrometry an extremely well suited tool in taking the step from single protein studies to high throughput structural biology on a genomic scale. This project is in particular concerned with flexible software that allows us to search mass fingerprints of peptides (and chemical modified peptides) quickly and reliable against large protein sequence databases.

  • Comparision of the 2nd virial from SAXS and force field calculations.
    Protein crystallisation is an essential step in protein structure determination by X-ray crystallography. Despite this importance, crystallisation still remains more an art than it is science. In this project we will directly compare experimentally accessible protein-protein interaction strength in form of the second virial from small angle light scattering (small angle X-ray scattering SAXS) with results from protein force field calculations.


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    The University of Queensland
    Brisbane, Queensland 4072 Australia
    Phone: +61 (7) 3365 7060
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    Authorised by: Director of ACMC
    Modified: 05 March 2002
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