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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
spectrometry
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
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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
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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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