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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. Publications |
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Abdelkader, E.H., Qianzhu, H., Otting, G. and Huber, T. Biosynthesis and genetic encoding of activated nitriles for fast protein conjugation and tunable fluorogenic labelling. Chem (2024) accepted.[Supplementary information] |
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Qianzhu, H., Abdelkader, E.H., Welegedara, A.P., Habel, E., Paul, N., Frkic, R.L., Jackson. C.J., Huber, T., Otting G. Rendering proteins fluorescent inconspicuously: genetically encoded 4-cyanotryptophan conserves their structure and enables the detection of ligand binding sites. Angew. Chem., Int. Ed., (2024) accepted. [Supplementary information] |
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Qianzhu, H., Abdelkader, E.H., Otting, G. and Huber, T. Genetic Encoding of Fluoro-L-tryptophans for Site-specific Detection of Conformational Heterogeneity in Proteins by NMR Spectroscopy. JACS (2024) 146 13641-13650.[Supplementary information] |
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Abdelkader, Qianzhu, H., Huber, T. and Otting, G. Genetic encoding of 7-aza-L-tryptophan: Isoelectronic substitution of a single CH-group in a protein for a nitrogen atom for site-selective isotope labeling ACS Sensors (2023) 8 4402-4406.[Supplementary information] |
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Maxwell, M., Tan, Y.J., Lee, R., Huber, T. and Otting, G. Electrostatic contribution to 19F chemical shifts in fluorotryptophans in proteins Biochemistry (2023) 62 3255-3264. [Supplementary information] |
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van Raad, D. and Huber, T.
eCell Technology for Cell-Free Protein Synthesis, Biosensing, and Remediation in Cell-free Macromolecular Synthesis (Eds. Yuan Lu and Michael C. Jewett) Springer Cham 2023. ISBN: 978-3-031-41286-8 |
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van Raad, D., Huber, T. and Otting, G. Improved spectral resolution of [13C,1H]-HSQC spectra of aromatic amino acid residues in proteins produced by cell-free synthesis from inexpensive 13C-labelled precursors J. Biomol. NMR (2023) 77 183-190. [Supplementary information] |
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van Raad, D., Otting, G. and Huber, T. Cell-free synthesis of proteins with selectively 13C-labelled methyl groups from inexpensive precursors Magn. Reson. (2023) 4 187-197. [Supplementary information] |
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Ekanayake, K.B., Mahawaththa, M.C., Qianzhu, H., Abdelkader, E.H., George, J., Ullrich, S., Murphy, R.B., Fry, S.E., Johansen-Leete, J., Payne, R.J., Nitsche, C., Huber, T. and Otting, G. Probing Ligand Binding Sites on Large Proteins by Nuclear Magnetic Resonance Spectroscopy of Genetically Encoded Non-Canonical Amino Acids. J.Med.Chem. (2023) 66 5289-5304.[Supplementary information] |
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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. |
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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. |
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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] |
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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] |
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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] |
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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. |
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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] |
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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 |
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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] |
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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] |
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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] |
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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. |
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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] |
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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 |
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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 |
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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] |
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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] |
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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 |
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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] |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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) 132 9040-9048. [Supplementary information] |
39 citations |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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Hamilton, N. and Huber, T.
An Introduction to Protein Contact Prediction in Bioinformatics (Ed. Keith, J.M.) Humana Press 2008. |
book chapter |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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Gladwin, B.A. and Huber, T.,
Long Time Scale Molecular Dynamics Using Least Action ANZIAM J. (2004) 45.C534--C550 |
1 citations |
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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 |
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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 |
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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 |
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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 |
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Huber, T.,
Bayesian classification of protein data. HPC Asia. (2001). |
0 citations |
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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 |
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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 |
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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 |
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Huber, T., Russell, A.J., Ayers, D, Torda, A.E.,
SAUSAGE: Protein threading with flexible force fields. Bioinformatics 15 (1999), 1064-1065. |
25 citations |
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Ayers, D., Huber, T. and Torda, A.E.,
Protein fold recognition force fields: unusual construction strategies. Proteins 36 (1999) 454-461. |
7 citations |
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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 |
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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 |
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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). |
conference proceeding |
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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 |
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Huber, T. and Torda, A.E.,
Protein fold recognition without Boltzmann statistics or explicit physical basis. Prot. Sci. 7 (1998) 1-8. |
33 citations |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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Huber, T. and Rendell, A.,
Molecular dynamics simulations using GRAPE/Wine hardware, June 1999. |
0 citations |
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