Professor Alan Mark - UQ reSEARCHers (Publications)

	Publications

	2012	Mimicking the action of folding chaperones by Hamiltonian replica-exchange molecular dynamics simulations: Application in the refinement of de novo models
	2012	Molecular dynamics unlocks atomic level self-assembly of the exopolysaccharide matrix of water-treatment granular biofilms
	2012	Missing fragments: Detecting cooperative binding in fragment-based drug design
	2012	Charge group partitioning in biomolecular simulation
	2011	An automated force field topology builder (ATB) and repository: Version 1.0
	2011	The effect of environment on the recognition and binding of vancomycin to native and resistant forms of lipid II
	2011	Protein a-turns recreated in structurally stable small molecules
	2011	A dynamic pharmacophore drives the interaction between psalmotoxin-1 and the putative drug target acid-sensing ion channel 1a
	2011	Comparison of enveloping distribution sampling and thermodynamic integration to calculate binding free energies of phenylethanolamine N-methyltransferase inhibitors
	2011	Definition and testing of the GROMOS force-field versions 54A7 and 54B7
	2011	Using theory to reconcile experiment : The structural and thermodynamic basis of ligand recognition by phenylethanolamine N -methyltransferase (PNMT)
	2011	The effect of membrane curvature on the conformation of antimicrobial peptides: Implications for binding and the mechanism of action
	2011	Effect of high pressure on fully hydrated DPPC and POPC bilayers
	2011	Effect of poly(ethylene glycol) (PEG) spacers on the conformational properties of small peptides: A molecular dynamics study
	2011	Challenges in the determination of the binding modes of non-standard ligands in X-ray crystal complexes
	2010	On the relative merits of equilibrium and non-equilibrium simulations for the estimation of free-energy differences
	2010	Activating the prolactin receptor: Effect of the ligand on the conformation of the extracellular domain
	2010	Basic ingredients of free energy calculations: A review
	2010	A new force field for simulating phosphatidylcholine bilayers
	2010	Turning the growth hormone receptor on: Evidence that hormone binding induces subunit rotation
	2010	On the validation of molecular dynamics simulations of saturated and cis-monounsaturated phosphatidylcholine lipid bilayers: A comparison with experiment
	2009	Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible
	2009	Alternative mechanisms for the interaction of the cell-penetrating peptides penetratin and the TAT peptide with lipid bilayers
	2009	Inclusion of ionization states of ligands in affinity calculations
	2009	Probing the free energy landscape of the FBP28WW domain using multiple techniques
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