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That swagman had a history, highly important, at all events, to himself.
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and if any human being wants a higher record than that, he must work for it.

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Potapov, A., Yagi, H., Huber, T., Jergic, S., Dixon, N.E., Otting G. and Goldfarb, D.
Nanometer-Scale Distance Measurements in Proteins Using Gd3+ Spin Labeling.
JACS (2010) . [Supplementary information]

0 citations
Yagi, H., Loscha, K.V., Su, X-C., Stanton-Cook, M.J., Huber, T. and Otting G.
Tunable paramagnetic relaxation enhancements by [Gd(DPA)3]3- for protein structure analysis
J. Biomol. NMR (2010) 47 143-153. [Supplementary information]

0 citation
Man, B., Su, X-C., Liang, H., Simonsen, S., Huber, T., Messerle, B.A. and Otting, G.
3-Mercapto-2,6-Pyridinedicarboxylic Acid: A Small Lanthanide-Binding Tag for Protein Studies by NMR Spectroscopy
Chem. Eur. J. (2010) 16 3827-3832. [Supplementary information]

0 citation
Li, R., Ding, T., Huber T., Falconer, R.J., Middelberg, A., Gladden, L.F. and Zeitler, J.A.
Terahertz time-domain spectroscopy of peptides in solution.
This paper appears in: Infrared, Millimeter, and Terahertz Waves, 2009. IRMMW-THz 2009. 34th International Conference on (2009), 1-2.

0 citations
Li, S, Mouradov, D., King, G., Liu, T., Ross, I., Kobe, B., Woods Jr, V.L. and Huber T.
Study of protein three-dimensional structure and dynamics using peptide amide hydrogen/deuterium exchange mass spectrometry (DXMS) and chemical cross-linking with mass spectrometry to constrain molecular modeling.
Chapter 7 in Structural Bioinformatics 2nd edition Wiley-Blackwell (2009).

book chapter
Kobe, B., Guncar, G., Buchholz, R., Huber, T. and Maco, B.
The Many Faces Of Platelet Glycoprotein Ibα - Thrombin Interaction.
Current Protein & Peptide Science (2009) 10 551-558.

0 citations
Kobe, B., Guncar, G., Buchholz, R., Huber T., Maco, B., Cowieson, N., Martin, J.L., Marfori, M. and Forwood, J.
Crystallography and protein-protein interactions: biological interfaces and crystal contacts.
Biochemical Society Transactions (2008) 36 1438-1441.

0 citations
Hadler, K.S, Huber, T., Cassady, I., Weber, J., Robinson, J., Burrows, A., Kelly, G., Guddat, L.W., Hume, D.A., Schenk G. and Flanagan, J.U.
Identification of a non-purple tartrate-resistant acid phosphatase: an evolutionary link to Ser/Thr protein phosphatases?
BMC Research Notes (2008) 1 78. [PDF]

1 citations
Su, X.-C., Man, B., Beeren, S., Liang, H., Simonsen, S., Schmitz, C., Huber, T., Messerle, B.A. and Otting, G.
A Dipicolinic Acid Tag for Rigid Lanthanide Tagging of Proteins and Paramagnetic NMR Spectroscopy.
JACS (2008) 130 10486-10487.

0 citations
Schmitz, C., Stanton-Cook, M.J., Su, X-C., Otting, G. and Huber, T.
Numbat: an interactive software tool for fitting deltaX-tensors to molecular coordinates using pseudocontact shifts
J. Biomol. NMR (2008) 41 179-189. [Supplementary information]

1 citation
Saunders, N.F.W., Brinkworth, R.I., Huber, T., Kemp, B.E. and Kobe, B.
Predikin and PredikinDB: a computational framework for the prediction of protein kinase peptide specificity and an associated database of phosphorylation sites
BMC Bioinformatics (2008) 9 245. [PDF]

0 citations
King, G.J., Jones, A., Kobe, B., Huber, T., Mouradov, D., Hume, D.A. and Ross, I.L.
Rapid identification of disulfide-containing chemical cross-links in proteins using MALDI-TOF/TOF-mass spectrometry.
Analytical Chemistry (2008) 80 5036-5043.

3 citation
Cowieson, N.P., King, G., Cookson, D., Ross, I., Huber, T., Hume, D.A., Kobe B., Martin, J.L.,
Cortactin adopts a globular conformation and bundles actin into sheets.
JBC (2008) 283 16187-16193. [Supplementary information]

6 citations
Su, X.-C., McAndrew, K., Huber, T., Otting, G.,
Lanthanide-Binding Peptides for NMR Measurements of Residual Dipolar Couplings and Paramagnetic Effects from Multiple Angles.
JACS (2008) 130 1681-1687. [Supplementary information]

3 citations
Jiangning Song, Zheng Yuan, Hao Tan, Thomas Huber and Kevin Burrage,
Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure.
Bioinformatics (2007) 23 3147-3154.

2 citations
John, M., Schmitz, C., Park, A-Y., Dixon, N.E., Huber, T. and Otting, G.
Sequence-specific and stereospecific assignment of methyl groups using paramagnetic lanthanides
JACS (2007) 129 13749-13757.

1 citations
Forwood, J.K., Thakur, A., Guncar, G., Marfori, M., Mouradov, D., Meng, W.N., Robinson, J., Huber, T., Kellie, S., Martin, J.L., Hume, D.A., and Kobe, B.
Structural basis for recruitment of tandem hotdog domains in acyl-CoA thioesterase 7 and its role in inflammation
PNAS (2007) 104 10382-10387.

11 citations
Flanagan, J.U. and Huber T.,
Structural evolution of the ABCB family of transporter proteins.
Evolutionary Bioinformatics (2007), 309-316.
[Figure 1][Figure 2]

0 citations
Mouradov D, King G, Ross I, Forwood JK, Hume DA, Sinz A, Martin JL, Kobe B and Huber T.
Protein structure determination using a combination of cross-linking, mass spectrometry and molecular modelling.
In Methods in Molecular Biology v. 426 Humana Press (2008).

book chapter
Meng W, Forwood JK, Guncar G, Robin G, Cowieson NP, Listwan P, Mouradov D, King G, Ross IL, Robinson J, Puri M, Hill JM, Kellie S, Huber T, Hume DA, Martin JL and Kobe B
Overview of the pipeline for structural and functional characterization of macrophage proteins at the University of Queensland.
In Methods in Molecular Biology v. 426 Humana Press (2008).

book chapter
Robin G, Cowieson NP, Guncar G, Forwood JK, Listwan P, Hume DA, Kobe B, Martin JL and Huber T
A general target selection method for crystallographic proteomics.
In Methods in Molecular Biology v. 426 Humana Press (2008).

book chapter
Su, X-C., Huber, T., Dixon, N.E. and Otting, G.
Site-Specific Labelling of Proteins with a Rigid Lanthanide-Binding Tag
ChemBioChem 7 (2006) 1599-1604.

4 citations
DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., Huber, T., Dalevi, D., Hu, P., Andersen, G.L.
greengenes: Chimera-checked 16S rRNA gene database and workbench compatible with ARB
Appl. Environ. Microbiol. (2006) 72 5069-5072.

165 citations
Puri, M., Robin, G., Cowieson, N., Forwood, J.K., Listwan, P., Guncar, G., Hu, G., Huber, T., Hume, D.A., Kobe, B., and Martin, J.L.
Focusing in on structural genomics: The University of Queensland structural biology pipeline
Biomolecular Engineering 23 281-289.

4 citations
Hamilton, N. and Huber, T.
An Introduction to Protein Contact Prediction
in Bioinformatics (Ed. Keith, J.M.) Humana Press 2008.

book chapter
Song, J., Burrage, K., Yuan, Z. and Huber, T.
Prediction of cis/trans isomerization in proteins using PSI-BLAST profiles and secondary structure information
BMC Bioinformatics (2006) 7 124. [PDF]

17 citations
Schmitz, C., John, M., Park, A.Y., Dixon, N.E., Otting, G., Pintacuda, G. and Huber, T.
Efficient chi-tensor determination and NH assignment of paramagnetic proteins
J. Biomol. NMR (2006) 35 79-87. [Supplementary information]

7 citations
Mouradov, D., Craven, A., Forwood, J., Flanagan, J., Garcia-Castellanos, R., Gomis-Ruth, F.X., Hume, D., Martin, J., Kobe, B. and Huber, T.
Modelling the structure of latexin-carboxypeptidase A complex based on chemical cross-linking and molecular docking
Protein Engineering, Design & Selection (2006) 19 9-16.

7 citations
Ozawa, K., Headlam, M.J., Mouradov, D., Watt, S.J., Beck, J.L., Rodgers, K.J., Dean, R.T., Huber, T., Otting, G. and Dixon, N.E.,
Translational incorporation of L-3,4-dihydroxyphenylalanine (DOPA) into proteins.
Eur. J. Biochem. (2005) 272 3162-3171.

14 citations
Cowieson, N., Listwan, P., Kurz, M., Aagaard, A., Ravasi, T., Wells, C., Huber, T., Hume, D.A., Kobe, B. and Martin, J.L.,
Pilot studies on the parallel production of soluble mouse proteins in a bacterial expression system.
J Struct Funct Genom (2005) 6 13-20.

5 citations
Aagaard, A., Listwan, P., Cowieson, N., Huber, T., Ravasi, T., Wells, C., Flanagan, J.U., Kellie, S., Hume, D.A., Kobe, B. and Martin, J.L.
An inflammatory role for the mammalian carboxypeptidase inhibitor latexin: relationship to cystatins and the tumour suppressor TIG1.
Structure (2005) 17 309-317.

22 citations
Pintacuda, G., Huber, T., Keniry, M., Park, Y.A, Dixon, N.E. and Otting, G.,
Fast assignments of 15N-HSQC spectra of proteins by paramagnetic labelling
Handbook of Modern Magnetic Resonance (2004).

book chapter
Huber, T. and Kobe, B.,
Comment on 'Protein Isoelectric Point as a Predictor for Increased Crystallization Screening Efficiency
Bioinformatics (2004) 20 2169-2170.

1 citations
Torda, A.E., Procter J. and Huber, T.,
Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices
Nucl. Acid Res. (2004) 32 W532-W535.

25 citations
Hamilton, N., Burrage, K., Ragan M.A. and Huber, T.,
Protein contact prediction using patterns of correlation
Proteins (2004) 56 (4), 679-684.

29 citations
Xu, Y., Zhang, R., Joachimiak, A., Carr, P.D., Huber, T., Vasudevan, S.G. and Ollis, D.,
Structure of the N-termial domain of Escherichia coli Glutamine Synthetase Adenylyltransferase
Structure (2004) 12, 861-869.

9 citations
Huber, T., Faulkner, G. and Hugenholtz, P.,
Bellerophon; a program to detect chimeric sequences in multiple sequence alignments
Bioinformatics (2004) 20, 2317-2319.

272 citations
Pintacuda, G., Keniry, M., Huber, T., Park, Y.A, Dixon, N.E. and Otting, G.,
Fast structure-based assignment of 15N-HSQC spectra of selectively labeled paramagnetic proteins
JACS (2004) 126, 2963-2970.

37 citations
Gladwin, B.A. and Huber, T.,
Long Time Scale Molecular Dynamics Using Least Action
ANZIAM J. (2004) 45.C534--C550

2 citations
Ravasi, T., Huber, T., Zavolan, M., Forrest, A.R.R., Gaasterland, T., Grimmond, S., RIKEN GER Group GSL Members and Hume, D.A.
Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome
Genome Research (2003) 13, 1430-1442.

32 citations
Forrest, A.R.R., Ravasi, T., Taylor, D., Huber, T., Hume, D.A., RIKEN GER Group GSL Members and Grimmond, S.,
Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse
Genome Research (2003) 13, 1443-1454.

20 citations
Hugenholtz, P. and Huber, T.,
Chimeric 16S rDNA sequences of diverse origin are accumulating in the public databases.
Int J Syst Evol Microbiol (2003) 53, 289-293.
(selected by Microbiology Today Editor Meriel Jones as a paper "which highlight new and exciting developments in microbiological research")

102 citations
Huber, T. and Torda, A.E.,
Protein structure prediction by threading: Force field philosophy, approaches to alignment.
in Protein Structure Prediction: A Bioinformatic Approach (Ed. Tsigelny, I.)
International University Line, La Jolla U.S.A. (2001).

book chapter
Huber, T.,
Bayesian classification of protein data.
HPC Asia. (2001).

0 citations
Xu, Y., Carr, P.D., Huber, T., Vasudevan, S.G., Ollis, D.L.,
The structure of the PII-ATP complex.
Eur. J. Biochem. (2001), 268,2028-2037.

34 citations
Reith, D., Huber, T., Müller-Plathe, F., Torda, A.E.,
Free Energy Approximations In Simple Lattice Proteins.
J. Chem. Phys. (2001) 114, 4998-5005.

6 citations
Rendell, A.P., Bliznyuk, A., Huber T., Nobes, R.H., Akhmatskaya, E.V., Früchtl, H.A., Kunk, P.W.-C., Milman, V.A., Lung, H.,
Computational chemistry on Fujitsu vector-parallel processors: Development and performance of application software.
Parallel Computing 26 (2000), 887-911.

4 citations
Huber, T., Russell, A.J., Ayers, D, Torda, A.E.,
SAUSAGE: Protein threading with flexible force fields.
Bioinformatics 15 (1999), 1064-1065.

18 citations
Ayers, D., Huber, T. and Torda, A.E.,
Protein fold recognition force fields: unusual construction strategies.
Proteins 36 (1999) 454-461.

6 citations
Huber, T. and Torda, A.E.,
Protein sequence threading, the alignment problem and a two step strategy.
J. Comp. Chem. 20 (1999) 1455-1467.

10 citations
Scott, W.R.P, Hünenberger, P.H., Tironi, I.G., Mark, A.E., Billeter, S.R., Fennen, J., Torda, A.E., Huber, T., Krüger, P. and van Gunsteren, W.F.,
The GROMOS biomolecular simulation program package.
J. Phys. Chem. A 103 (1999) 3596-3607.

403 citations
Rendell, A., Bliznyuk A, Huber, T., Gready J., Greatbanks, S. and Schmidt,R.,
Hybrid quantum mechanical/molecular mechanical (QM/MM) studies of enzyme reaction mechanisms: Building the computational engine.
HPC Asia (1998).

Huber, T. and van Gunsteren, W.F.,
SWARM-MD: searching conformational space by cooperative molecular dynamics.
J. Phys. Chem. A 102 (1998) 5937-5943.

24 citations
Huber, T. and Torda, A.E.,
Protein fold recognition without Boltzmann statistics or explicit physical basis.
Prot. Sci. 7 (1998) 1-8.

26 citations
Huber, T., Torda, A.E. and van Gunsteren, W.F.,
Structure optimisation combining soft-core interaction functions, the diffusion equation method and molecular dynamics.
J. Phys. Chem. A 101 (1997) 5926-5930.

23 citations
Nanzer, P.A., Huber, T., Torda, A.E., van Gunsteren, W.F.,
Molecular dynamics simulation using weak-coupling NOE distance restraining.
J. Biomol. NMR 8 (1996) 285-291.

3 citations
Huber, T., Torda, A.E., van Gunsteren, W.F.,
Optimization methods for conformational sampling using a Boltzmann weighted mean field approach.
Biopolymers 39 (1996), 103-114.

14 citations
van Gunsteren W.F., Huber T., Torda A.E.,
Biomolecular modelling: Overview of types of methods to search and sample conformational space,
Proceedings of the 1st European Conference on Computational Chemistry,
American Institute of Physics Conf. Proc., New York (1994).

8 citations
Huber T., Torda A.E., van Gunsteren W.F.,
Local Elevation: A method for improving the searching properties of molecular dynamics,
J. Comp.-Aided Mol. Design, 8 (1994), 695-708.

69 citations
Mierke D.F., Huber T., Kessler H.,
Coupling constants again: Experimental restraints in structure refinement,
J. Comp.-Aided Mol. Design, 8 (1994), 29-40.

13 citations
Torda A.E., Brunne R.M., Huber T., Kessler H., van Gunsteren W.F.,
Structure refinement using time averaged J-coupling constant restraints,
J. Biomol. NMR, 3 (1993), 55-66.

49 citations

Technical reports (not refereed) of possible interest to other people
Huber, T. and Rendell, A.,
Molecular dynamics simulations using GRAPE/Wine hardware,
June 1999.

0 citations

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