Biomolecular Modelling and Computational Biology Group


That swagman had a history, highly important, at all events, to himself.
He had been born; he lived; he would probably die -
and if any human being wants a higher record than that, he must work for it.

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Dowman, L.J., Kulkarni, S.S., Alegre-Requena, J.V., Giltrap, A.M., Norman, A.R., Sharma, A., Gallegos, L.C., Mackay, A.S., Welegedara, A.P., Watson, E.E., van Raad, D., Niederacher, G., Huhmann, S., Proschogo, N., Patel, K., Larance, M., Becker, C.F. W., Mackay, J.P., Lakhwani, G., Huber, T., Paton, R.S. and Payne, R.J.
Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine.
Nat.Commun. (2022) 13 6885.

0 citations
M. Judd, E. H. Abdelkader, M. Qi, J. R. Harmer, T. Huber, A. Godt, A. Savitsky, G. Otting and N. Cox
Short-range ENDOR distance measurements between Gd(III) and trifluoromethyl labels in proteins.
Phys.Chem.Chem.Phys. (2022) 24 25214-25226.

0 citations
Tharayil, S.M., Mahawaththa, M.C.,Feintuch, A., Maleckis, A., Ullrich, S., Morewood, R., Maxwell, M.J., Huber, T., Nitsche, C., Goldfarb, D. and Otting, G.
Site-selective generation of lanthanoid binding sites on proteins using 4-fluoro-2,6-dicyanopyridine.
Magn. Reson. (2022) 3 169-182. [Supplementary information]

0 citations
Abdelkader, E.H., Qianzhu, H., George, J., Frkic, R.L., Jackson. C.J., Nitsche, C., Otting G. and Huber, T.
Genetic encoding of cyanopyridylalanine for in-cell protein macrocyclization by the nitrile-aminothiol click reaction.
Angew. Chem., Int. Ed., (2022) 61 e202114154. [Supplementary information]

0 citations
Qianzhu, H., Abdelkader, E.H., Herath, I.D., Otting, G. and Huber, T.
Site-Specific Incorporation of 7-Fluoro-L-tryptophan into Proteins by Genetic Encoding to Monitor Ligand Binding by 19F NMR Spectroscopy.
ACS Sensors (2022) 7 44-49.[Supplementary information]

0 citations
Mahawaththa, M.C., Orton, H.W., Adekoya, I., Huber, T., Otting, G. and Nitsche, C.
Organoarsenic probes to study proteins by NMR spectroscopy.
Chem.Comm. (2022) 58 701-704.

0 citations
Orton, H.W., Qianzhu, H., Abdelkader, E.H., Habel, E.I., Tan, Y.J., Frkic, R.L., Jackson, C.J., Huber, T. and Otting, G.
Through-Space Scalar 19F-19F Couplings between Fluorinated Noncanonical Amino Acids for the Detection of Specific Contacts in Proteins.
JACS (2021) 143 19587-19598.[Supplementary information]

0 citations
Van Raad, D. and Huber, T.
In-vitro Protein Synthesis in Semi-Permeable Artificial cells.
ACS Synthetic Biology (2021) 10 1237-1244.[Supplementary information]

Associated patent: WO/2020/150789 Encapsulated Cells

0 citations
Abdelkader, E.H., Qianzhu, H., Tan, Y.J., Adams, L.A., Huber, T. and Otting, G.
Genetic Encoding of N6-(((Trimethylsilyl)methoxy)carbonyl)-l-lysine for NMR Studies of Protein-Protein and Protein-Ligand Interactions.
JACS (2021) 143 1133-1143.[Supplementary information]

0 citations
Welegedara, A.P., Maleckis, A., Bandara, R., Mahawaththa, M.C., Herath, I.D., Tan, Y.J., Giannoulis, A., Goldfarb, D. Otting, G. and Huber, T.
Cell-free synthesis of selenoproteins in high yield and purity for selective protein tagging.
ChemBioChem (2021) 22 1480-1486.[Supplementary information]

0 citations
Qianzhu, H., Welegedara, A., Williamson, H., McGrath, A., Mahawaththa, M., Dixon, N., Otting, G. and Huber, T.
Genetic Encoding of para-Pentafluorosulfanyl Phenylalanine: A Highly Hydrophobic and Strongly Electronegative Group for Stable Protein Interactions.
JACS (2020) 142 17277-17281.[Supplementary information]

0 citations
Koehler Leman, J., Weitzner, B. D., Lewis, S. M., Rosetta Consortium, R. and Bonneau, R.
Macromolecular Modeling and Design in Rosetta: New Methods and Frameworks.
Nature Methods (2020) 17 665-680.

0 citations
Koehler Leman, J., Weitzner, B. D., Renfrew, P. D., Lewis, S. M., Moretti, R., Watkins, A. M., Mulligan, V. K., Lyskov, S., Adolf-Bryfogle, J., Labonte, J. W., Rosetta Consortium, Bystroff, C., Schief, W., Schueler-Furman, O., Baker, D., Bradley, P., Dunbrack, R., Kortemme, T., Leaver-Fay, A., Strauss, C. E., Meiler, J., Kuhlman, B., Gray, J. J. & Bonneau, R.
Better together: Elements of successful scientific software development in distributed collaborative community.
PlosCompBio (2020) 16 e1007507. [full version]

0 citations
Orton, H. W., Huber, T. and Otting, G.
Paramagy: software for fitting magnetic susceptibility tensors using paramagnetic effects measured in NMR spectra.
Magn. Reson. (2020) 1 1-12. [Supplementary information]

0 citations
Su, X-C. and Huber, T.
In-cell Structure Determination Using Paramagnetic NMR Spectroscopy
in In-cell Nmr Spectroscopy: From Molecular Sciences To Cell Biology (Eds. Yutaka Ito, Volker Dötsch, Masahiro Shirakawa) Royal Society of Chemistry 2019. ISBN: 9781788012171

book chapter 
Yardeni, E.H., Bahrenberg, T., Stein, R.A., Mishra, S., Zomot, E., Graham, B., Tuck, K.L., Huber, T., Bibi, E., Mchaourab, H.S. and Goldfarb, D.
Probing the solution structure of the E. coli multidrug transporter MdfA using DEER distance measurements with nitroxide and Gd(III) spin labels.
Scientific Reports (2019) 9 12528. [Supplementary information]

0 citations
Bahramzadeh, A, Huber, T. and Otting, G.
Three-Dimensional Protein Structure Determination Using Pseudocontact Shifts of Backbone Amide Protons Generated by Double-Histidine Co2+-Binding Motifs at Multiple Sites.
Biochemistry (2019) 58 3243-3250. [Supplementary information]

0 citations
Nitsche, C., Onagi, H. Quek, J-P., Otting, G. Luo, D. and Huber, T.
Biocompatible Macrocyclization between Cysteine and 2-Cyanopyridine Generates Stable Peptide Inhibitors.
Org. Lett. (2019) 21 4709-4712. [Supplementary information]

0 citations
Welegedara, A., Adams, L.A., Huber, T., Graham, B. and Otting, G.
Site-specific incorporation of selenocysteine by genetic encoding as a photocaged unnatural amino acid.
Bioconjugate Chem. (2018) 29 2257-2264. [Supplementary information]

0 citations
Bahramzadeh, A., Jiang, H., Huber, T. and Otting G.
Two Histidines in an α-Helix: A Rigid Co2+-Binding Motif for PCS Measurements by NMR Spectroscopy.
Angew. Chem., Int. Ed., (2018) 57 6226-6229. [Supplementary information]

0 citations
Kirk, J., Huber, T. and Jackson, C.J.
Modulating Enzyme Activity via Incorporation of Non-canonical Amino Acids
in Modern Biocatalysis: Advances Towards Synthetic Biological Systems (Eds. Gavin Williams, Melanie Hall) Royal Society of Chemistry 2018. ISBN: 9781782627265

book chapter 
Nitsche, C., Mahawaththa, M.C., Becker, W., Huber, T. and Otting, G.
Site-selective tagging of proteins by pnictogen-mediated self-assembly.
Chem.Comm. (2017) 53 10894-10897.[Supplementary information]

0 citations
Welegedara, A.P., Yang, Y., Lee, M.D., Swarbrick, J.D., Huber, T., Graham, B., Goldfarb, D. and Otting, G.
Double-arm lanthanide tags deliver narrow Gd3+-Gd3+ distance distributions in DEER measurements.
Chem. Eur. J. (2017) 23 11694-11702. [Supplementary information]

0 citations
Pilla, K.B., Otting, G. and Huber T.
Protein structure determination by assembling super-secondary structure motifs using pseudocontact shifts.
Structure (2017) 25 559-568. [Supplementary information]

0 citations
Pan, B.-B., Yang, F., Ye, Y., Wu, Q., Li, C, Huber, T., and Su, X.-C.
3D structure determination of a protein in living cells using paramagnetic NMR spectroscopy.
Chem.Comm. (2016) 52 10237-10240.[Supplementary information]

0 citations
Chen, W-N., Nitsche, C., Pilla, K.B., Graham, B., Huber, T., Klein, C.D. and Otting, G.
Sensitive NMR approach for determining the binding mode of tightly binding ligand molecules to protein targets.
JACS (2016) 138 4539-4546.[Supplementary information]

0 citations
Pilla, K.B, , Otting, G. and Huber, T.
Pseudocontact Shift-Driven Iterative Resampling for 3D Structure Determinations of Large Proteins.
J.Mol.Biol. (2016) 428 522-532. [Supplementary information]

0 citations
Yang, Y., Huang, F., Huber, T. and Su, X.-C.
Site-specific tagging proteins with a rigid, small and stable transition metal chelator, 8-hydroxyquinoline, for paramagnetic NMR analysis.
J. Biomol. NMR (2016) 64 103-113.

0 citations
Pilla, K.B, , Otting, G. and Huber, T.
3D computational modelling of proteins using sparse paramagnetic NMR data
in Bioinformatics Vol. II (Ed. Keith, J.M.) Methods in Molecular Biology, Springer Protocols 2016.

book chapter 
Chen, J.-L., Yang, Y., Zhang, L.-L., Linag, H., Huber, T., Su, X.-C. and Otting, G.
Analysis of the solution conformations of T4 lysozyme by paramagnetic NMR spectroscopy.
Phys. Chem. Chem. Phys. (2016) 18 5850-5859.

0 citations
Zhao, Y, Soh, T.S., Chan, K.W.K., Fung, S.S.Y., Swaminathan, K., Lim, S.P., Shi, P.-Y., Huber, T., Lescar, J., Luo, D. and Vasudevan, S.G.
Flexibility of NS5 Methyltransferase-Polymerase Linker Region is Essential for Dengue virus Replication.
J. Virol. (2015) 89 10717-10721.

0 citations
Pilla, K.B, Koehler Leman, J., Otting, G. and Huber, T.
Capturing conformational states in proteins using sparse paramagnetic NMR data.
PLoS One (2015) 10 e0127053 (16 pages).

0 citations
Chen, W-N., Kuppan, K., Lee, M., Jaudzems, K., Huber, T. and Otting, G.
O-tert-Butyltyrosine, an NMR tag for high-molecular weight systems and measurements of submicromolar ligand binding affinities.
JACS (2015) 137 4581-4586. [Supplementary information]

0 citations
Porter, J.L., Boon, P.L.S., T.P. Murray, Huber T., Collyer, C.A. and Ollis D.L.
Directed Evolution of New and Improved Enzyme Functions Using an Evolutionary Intermediate and Multi-directional Search.
ACS Chem. Biol. (2015) 10 611-621.

0 citations
Edwards, D.T., Huber T., Hussain, S., Stone, K.M., Kinnebrew, M., Kaminker, I., Matalon, E., Sherwin, M.S., Goldfarb, D. and Han, S.
Determining the oligomeric structure of proteorhodopsin by Gd3+-based pulsed dipolar spectroscopy of multiple distances.
Structure (2014) 22 1677-1686. [Supplementary information]

0 citations
Skarshewski, A., Stanton-Cook, M., Huber, T., Al Mansoori, S., Smith, R., Beatson, S.A. and Rothnagel, J.A.
uPEPperoni: An online tool for upstream open reading frame location and analysis of transcript conservation.
BMC Bioinformatics (2014) 15 36 (6 pages).

1 citation
Shishmarev, D., Wang, Y., Mason, C.E., Su, X-C., Oakley, A.J., Graham, B., Huber, T., Dixon, N.E. and Otting G.
Intramolecular binding mode of the C-terminus of Escherichia coli single-stranded DNA binding protein determined by nuclear magnetic resonance spectroscopy.
Nucl. Acid Res. (2014) 42 2750-2757. [Supplementary information]

1 citation
Milthorpe, J., Rendell, A.P. and Huber, T.
PGAS-FMM: Implementing a distributed fast multipole method using the X10 programming language.
Concurrency Computat.: Pract. Exper. (2014) 26 712-727.

2 citations
Matalon, E., Huber, T., Hagelueken, G., Graham, B., Frydman, V., Feintuch, A., Otting G. and Goldfarb D.
Gd3+ Spin Labels for High Sensitivity Distance Measurements in Trans-Membrane Helices.
Angew. Chem., Int. Ed., (2013) 54 11831-11834. [Supplementary information]

3 citations
Li, J., Pilla, K.B., Li, Q., Zhang, Z., Su, X., Huber, T. and Yang, J
Magic Angle Spinning NMR Structure Determination of Proteins from Pseudocontact Shifts.
JACS (2013) 135 8294-8303. [Supplementary information]

5 citations
Yagi, H., Pilla, K.B., Maleckis, A., Graham, B., Huber T. and Otting, G.
3D Protein Fold Determination from Backbone Amide Pseudocontact Shifts Generated by Lanthanide Tags at Multiple Sites.
Structure (2013) 21 883-890. [Supplementary information]

3 citations
Ozawa, K., Horan, N.P., Robinson, A., Yagi, H., Hill, F.R., Jergic, S., Xu, Z.Q., Loscha, K.V., Li, N., Tehei, M., Oakley, A.J., Otting, G., Huber T. and Dixon, N.E.
Proofreading exonuclease on a tether: the complex between the E. coli DNA polymerase III subunits α, ε, θ and β reveals a highly flexible arrangement of the proofreading domain.
Nucl. Acid Res. (2013) 41 5354-5367. [Supplementary information]

2 citations
Jergic, S., Horan, N.P., Elshenawy, M.M., Mason, C.E., Urathamakul, T., Ozawa, K., Robinson, A., Goudsmits, J.M.H., Wang, Y., Pan, X., Beck, J.L., van Oijen, A.M., Huber, T., Hamdan, S.M. and Dixon, N.E.
A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode.
EMBO J. (2013) 32 1322-1333. [Supplementary information]

7 citations
Loh, C.T., Ozawa, K., Tuck, K.L., Barlow, N., Huber, T., T., Otting, G. and Graham, B.
Lanthanide Tags for Site-Specific Ligation to an Unnatural Amino Acid and Generation of Pseudocontact Shifts in Proteins.
Bioconjugate Chem. (2013) 24 260-268. [Supplementary information]

9 citations
Kaminker, I., Tkach, I., Manukovsky, N., Huber, T., Yagi, H.,Otting, G., Bennati, M. and Goldfarb D.
W-band orientation selective DEER measurements on a Gd3+/nitroxide mixed-labeled protein dimer with a dual mode cavity.
J. Mag. Res. (2013) 227 66-71.[Supplementary information]

8 citations
Ding, T., Middelberg, A.P.J., Huber, T. and Falconer R.J.
Far-infrared spectroscopy analysis of linear and cyclic peptides, and lysozyme.
Vib. Spectrosc. (2012) 61 144-150.

6 citations
Kaminker, I., Yagi, H., Huber, T., Feintuch, A., Otting, G. and Goldfarb, D.
Spectroscopic selection of distance measurements in a protein dimer with mixed nitroxide and Gd3+ spin labels.
Phys. Chem. Chem. Phys. (2012) 14 4355-4358.

21 citations
Loscha, K.V., Herlt, A.J., Qi, R., Huber, T., Ozawa, K. and Otting, G.
Multi-site labeling of proteins with unnatural amino acids.
Angew. Chem., Int. Ed., (2012) 51 2243-2246. [Supplementary information]

22 citations
Schmitz, C., Vernon, R., Otting, G., Baker, D. and Huber, T.
Protein structure determination from pseudocontact shifts using ROSETTA.
J. Mol. Biol. (2012) 416 668-677. [Supplementary information]

21 citations
Banerjee, D., Yagi, H., Huber, T., Otting, G., Goldfarb, D.
Nanometer range distance measurement in a protein using Mn2+ tags.
J. Phys. Chem. Lett. (2012) 3 157-160. [Supplementary information]

8 citations
de la Cruz, L., Nguyen, T.H.D., Ozawa, K., Shin, J., Graham, B., Huber, T. and Otting G.
Binding of Low Molecular Weight Inhibitors Promotes Large Conformational Changes in the Dengue Virus NS2B-NS3 Protease: Fold Analysis by Pseudocontact Shifts.
JACS (2011) 133 19205-19215. [Supplementary information]

21 citations
Ding, T., Huber, T., Middelberg, A.P.J. and Falconer R.J.
Characterization of Low-Frequency Modes in Aqueous Peptides Using Far-Infrared Spectroscopy and Molecular Dynamics Simulation.
J.Phys.Chem. A (2011) 115 11559-11565. [Supplementary information]

11 citations
Graham, B., Loh, C.T., Swarbrick, J.D., Ung, P., Shin, J., Yagi, H., Jia, X., Chhabra, S., Barlow, N., Pintacuda, G., Huber, T. and Otting, G.
DOTA-Amide Lanthanide Tag for Reliable Generation of Pseudocontact Shifts in Protein NMR Spectra.
Bioconjugate Chem. (2011) 22 2118-2125. [Supplementary information]

26 citations
Yagi, H., Banerjee, D., Graham, B., Huber, T., Goldfarb, D. and Otting G.
Gadolinium Tagging for High-Precision Measurements of 6 nm Distances in Protein Assemblies by EPR.
JACS (2011) 133 10418-10421. [Supplementary information]

34 citations
Jia, X., Yagi, H., Su, X.-C., Stanton-Cook, M.J., Huber, T. and Otting G.
Engineering [Ln(DPA)(3)](3-) binding sites in proteins: a widely applicable method for tagging proteins with lanthanide ions
J. Biomol. NMR (2011) 50 411-420. [Supplementary information]

13 citations
Swarbrick, J.D., Ung, P. Su, X-C., Maleckis, A., Chhabra, S., Huber, T., Otting, G. and Graham, B.
Engineering of a bis-chelator motif into a protein α-helix for rigid lanthanide binding and paramagnetic NMR spectroscopy.
ChemComm. (2011) 47 7368-7370.

16 citations
Jia,X., Maleckis, A., Huber, T. and Otting G.
4,4'-Dithiobis-dipicolinic acid: a small and convenient lanthanide binding-tag for protein NMR spectroscopy.
Chem. Eur. J. (2011) 17 6830-6836.[Supplementary information]

10 citations
Ding, T., Li, R., Zeitler, J.A., Huber, T. , Gladden, L.F., Middelberg, A.P.J and Falconer, R.J.
Terahertz and far infrared Spectroscopy of alanine-rich peptides having variable ellipticity.
Optics Express (2010) 18 27431-27444.

20 citations
Nguyen, T.H.D, Ozawa, K., Stanton-Cook, M., Barrow, R., Huber, T. and Otting, G.
Generation of Pseudocontact Shifts in Protein NMR Spectra with a Genetically Encoded Cobalt(II)-Binding Amino Acid.
Angewandte Chemie (2011) 50 692-694. [Supplementary information]

12 citations
Mouradov, D., Kobe, B., Dixon N.E. and Huber T.
Hybrid methods for protein structure prediction.
Chapter 12 in Protein Structure Methods and Algorithms , Wiley (2010).
TOC and preface

book chapter 
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) 132 9040-9048. [Supplementary information]

39 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]

8 citations
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]

22 citations
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.

5 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.

25 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]

6 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.

62 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]

57 citations
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]

38 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.

21 citations
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]

21 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]

52 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.

53 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. [Supplementary information]

22 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.

44 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]

4 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.

57 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.

1502 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.

10 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]

55 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]

35 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.

16 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.

33 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.

8 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.

48 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.

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

68 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.

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

1132 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.

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

1 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.

73 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.

39 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")

190 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.

53 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.

5 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.

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

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

7 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.

11 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.

946 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.

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

33 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.

35 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.

8 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.

25 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).

16 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.

231 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.

21 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.

100 citations
Huber, T. and Rendell, A.,
Molecular dynamics simulations using GRAPE/Wine hardware,
June 1999.

0 citations

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