Department of Chemestry
Publications by Andrew Torda
.
| Search: Chemistry Dep. / all Hamburg | |
| 2025 | |
| 86 |
A universal DNA microarray for rapid fish species authentication Patrizia Bade, Sebastian Stix, Kristina Kappel, Jan Fritsche , Ilka Haase, Andrew E. Torda , Nils Wax, Markus Fischer , Dirk Brandis, Ute Schröder Food Chemistry: Molecular Sciences 10, 100241 (11 pp) (2025) |
2024 | |
| 85 |
Differentiable partition function calculation for RNA Marco C. Matthies, Ryan Krueger, Andrew E. Torda , Max Ward Nucleic Acids Research 52, e14 (9 pp) (2024) |
2023 | |
| 84 |
Conserved intramolecular networks in GDAP1 are closely connected to CMT-linked mutations and protein stability Aleksi Sutinen, Dirk Paffenholz, Giang Thi Tuyet Nguyen, Salla Ruskamo, Andrew E. Torda , Petri Kursula PLoS One 18, e0284532 (29 pp) (2023) |
2021 | |
| 83 |
Proteins Binding to the Carbohydrate HNK-1: Common Origins? Gaston Castillo, Ralf Kleene, Melitta Schachner, Gabriele Loers, Andrew E. Torda International Journal of Molecular Sciences 22, 8116 (11 pp) (2021) |
| 82 |
Repurposing tRNAs for nonsense suppression Suki Albers , Bertrand Beckert, Marco C. Matthies, Chandra Sekhar Mandava, Raphael Schuster, Carolin Seuring , Maria Riedner , Suparna Sanyal, Andrew E. Torda , Daniel N. Wilson , Zoya Ignatova Nature Communications 12, 3850 (10 pp) (2021) |
| 81 |
Crystal and solution structures reveal oligomerization of individual capsid homology domains of Drosophila Arc Erik I. Hallin, Sigurbjörn Markússon, Lev Böttger, Andrew E. Torda , Clive R. Bramham, Petri Kursula PLoS One 16, e0251459 (26 pp) (2021) |
2020 | |
| 80 |
Synthetic transfer RNA with extended anticodon loop Zoya Ignatova , Andrew E. Torda -/- Applicants: Universität Hamburg Patent: WO 2020208169 (A1) 2020-10-15 |
2019 | |
| 79 |
Improving the Numerical Stability of the NAST Force Field for RNA Simulations Nils P. Petersen, Thomas Ort, Andrew E. Torda Journal of Chemical Theory and Computation 15, 3402-3409 (2019) |
| 78 |
Synthetic transfer RNA with extended anticodon loop Zoya Ignatova , Andrew E. Torda , Marco Matthies -/- Applicants: Universität Hamburg Patent: WO 2019175316 (A1) 2019-09-19 |
2018 | |
| 77 |
Antibiotikaresistenz, Evolution und Darwins Magenkrämpfe Andrew E. Torda , Barbara M. Schwarz Update Antibiotikaresistenz: Entstehung, Epidemiologie, Wirkstoffentwicklung 45-49 (2018), ISBN 978-3-7692-7113-3 , Publisher: Deutscher Apotheker Verlag |
2016 | |
| 76 |
Structural and functional evolution of 2',3'-cyclic nucleotide 3'-phosphodiesterase Matti Myllykoski, Leonie Seidel, Gopinath Muruganandam, Arne Raasakka, Andrew E. Torda , Petri Kursula Brain Research 1641A, 64-78 (2016) |
| 75 |
The Crystal Structure of the C-Terminal Domain of the Salmonella enterica PduO Protein: An Old Fold with a New Heme-Binding Mode Dario Ortiz de Orué Lucana, Neal Hickey, Michael Hensel, Johann P. Klare, Silvano Geremia, Tatiana Tiufiakova, Andrew E. Torda Frontiers in Microbiology 7, 1010 (2016) |
| 74 |
Genomes: At the edge of chaos with maximum information capacity Sing-Guan Kong, Hong-Da Chen, Andrew E. Torda , H. C. Lee International Journal of Modern Physics B 30, 1550255 (2016) |
2015 | |
| 73 |
Two independently folding units of Plasmodium profilin suggest evolution via gene fusion Saligram Prabhakar Bhargav, Juha Vahokoski, Juha Pekka Kallio, Andrew E. Torda , Petri Kursula, Inari Kursula Cellular and Molecular Life Sciences 72, 4193-4203 (2015) |
| 72 |
The LUX Score: A Metric for Lipidome Homology Chakravarthy Marella, Andrew E. Torda , Dominik Schwudke PLoS Computational Biology 10, e1004511 (20 pp) (2015) Reprint: bioRxiv, Bioinformatics 13847 |
2014 | |
| 71 |
Not assessing the efficiency of multiple sequence alignment programs Andrew E. Torda Algorithms for Molecular Biology 9, 18 (2014) |
| 70 |
The Extracellular Heme-binding Protein HbpS from the Soil Bacterium Streptomyces reticuli Is an Aquo-cobalamin Binder Dario Ortiz de Orué Lucana, Sergey N. Fedosov, Ina Wedderhoff, Edith N. Che, Andrew E. Torda Journal of Biological Chemistry 289, 34214-34228 (2014) |
| 69 |
RNA
aptamer design Cindy Meyer, Ulrich Hahn , Andrew E. Torda -/- Editor: Gisbert Schneider De Novo Molecular Design 519-542 (2014), ISBN 978-3-527-33461-2 |
| 68 |
Applications of Structural Biology and Bioinformatics in the Investigation of Oxidative Stress-Related Processes Beate Bersch, Matthew R. Groves, Johann P. Klare, Andrew E. Torda , Dario Ortiz de Orué Lucana -/- Editor: Ismail Laher Systems Biology of Free Radicals and Antioxidants 505-534 (2014) |
2013 | |
| 67 |
Fast alignment and comparison of RNA structures Tim Wiegels, Stefan Bienert, Andrew E. Torda Bioinformatics 29, 588-596 (2013) |
| 66 |
RNA secondary structure diagrams for very large molecules: RNAfdl Nikolai Hecker, Tim Wiegels, Andrew E. Torda Bioinformatics 29, 2941-2942 (2013) |
| 65 |
Elucidation of haem-binding sites in the actinobacterial protein HbpS Andrew E. Torda , Matthew R. Groves, Ina Wedderhoff, Dario Ortiz de Orué Lucana FEMS Microbiology Letters 342, 106-112 (2013) |
| 64 |
Site directed immobilization of glucose-6-phosphate dehydrogenase via thiol-disulfide interchange: Influence on catalytic activity of cysteines introduced at different positions Jan R. Simons, Martin Mosisch, Andrew E. Torda , Lutz Hilterhaus Journal of Biotechnology 167, 1-7 (2013) |
| 63 |
d(GGGT)4 and r(GGGU)4 are both HIV-1 inhibitors and interleukin-6 receptor aptamers Eileen Magbanua, Tijana Zivkovic, Björn Hansen, Niklas Beschorner, Cindy Meyer, Inken Lorenzen, Joachim Grötzinger, Joachim Hauber, Andrew E. Torda , Günter Mayer, Stefan Rose-John, Ulrich Hahn RNA Biology 10, 216-227 (2013) |
| 62 |
d(GGGT)4 and r(GGGU)4 are both HIV-1 inhibitors and interleukin-6 receptor aptamers Eileen Magbanua, Tijana Zivkovic, Björn Hansen, Niklas Beschorner, Cindy Meyer, Inken Lorenzen, Joachim Grötzinger, Joachim Hauber, Andrew E. Torda , Günter Mayer, Stefan Rose-John, Ulrich Hahn RNA Biology 10 (2) 216-227 (2013) |
2012 | |
| 61 |
Dynamics in Sequence Space for RNA Secondary Structure Design Marco C. Matthies, Stefan Bienert, Andrew E. Torda Journal of Chemical Theory and Computation 8, 3663-3670 (2012) |
2010 | |
| 60 |
RNA secondary structure prediction using a self-consistent mean field approach Jens Kleesiek, Andrew E. Torda Journal of Computational Chemistry 31, 1135-1142 (2010) |
2009 | |
| 59 |
The SALAMI protein structure search server Thomas Margraf, Gundolf Schenk, Andrew E. Torda Nucleic Acids Research 37 (Suppl. 2) W480-W484 (2009) |
| 58 |
Quantitative measure of randomness and order for complete genomes Sing-Guan Kong, Wen-Lang Fan, Hong-Da Chen, Jan Wigger, Andrew E. Torda , H. C. Lee Physical Review E: Statistical, Nonlinear, and Soft Matter Physics 79, 061911/1-061911/11 (2009) |
2008 | |
| 57 |
Protein sequence and structure alignments within one framework Gundolf Schenk, Thomas Margraf, Andrew E. Torda Algorithms for Molecular Biology 3, 4 (2008) |
| 56 |
Characterization of the Quinolone-Gyrase-Interaction Using Docking, Molecular-Dynamics and Site-Directed Mutagenesis Jörn Lenz, Thomas Lemcke, Peter Heisig, Andrew E. Torda -/- Editor: Ulrich H. E. Hansmann, Jan H. Meinke, Sandipan Mohanty, Walter Nadler, Olav Zimmermann From Computational Biophysics to Systems Biology (CBSB08). Proceedings of the NIC Workshop 2008, 40, 289-292 (2008), ISBN 978-3-9810843-6-8 , Publisher: John von Neumann Institute for Computing, Jülich |
2007 | |
| 55 |
Genomes: at the edge of chaos with maximum information capacity Sing-Guan Kong, Hong-Da Chen, Wen-Lang Fan, Jan Wigger, Andrew E. Torda , H. C. Lee Los Alamos National Laboratory, Preprint Archive, Quantitative Biology 1-4, arXiv:0708.1598v1 [q-bio.GN] (2007) |
2006 | |
| 54 |
Editorial Andrew E. Torda , Thomas Lengauer Bioinformatics 22, 1157-1157 (2006) |
| 53 |
Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces Phuong H. Nguyen, Emil Mittag, Andrew E. Torda , Gerhard Stock Journal of Chemical Physics 124, 154107/1-154107/6 (2006) |
2005 | |
| 52 |
Functional analysis of the methylmalonyl-CoA epimerase from Caenorhabditis elegans Jochen Kühnl, Thomas Bobik, James B. Procter, Cora Burmeister, Jana Höppner, Inga Wilde, Kai Lüersen, Andrew E. Torda , Rolf D. Walter, Eva Liebau FEBS Journal 272, 1465-1477 (2005) |
| 51 |
The Highly Abundant Protein Ag-lbp55 from Ascaridia galli Represents a Novel Type of Lipid-binding Proteins Rositsa Jordanova, Georgi Radoslavov, Peter Fischer, Andrew E. Torda , Friedrich Lottspeich, Raina Boteva, Rolf D. Walter, Ilia Bankov, Eva Liebau Journal of Biological Chemistry 280, 41429-41438 (2005) |
| 50 |
German Conference on Bioinformatics GCB 2005, Hamburg, Germany, October 5-7, 2005 Editors: Andrew E. Torda , Stefan Kurtz , Matthias Rarey |
| 49 |
Protein Threading Andrew E. Torda -/- Editor: J. M. Walker Proteomics Protocols Handbook 921-938 (2005) |
2004 | |
| 48 |
Wurst: A protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices Andrew E. Torda , James B. Procter, Thomas Huber Nucleic Acids Research 32 (Suppl. 2) W532-W535 (2004) |
| 47 |
New enzymes from environmental cassette arrays: Functional attributes of a phosphotransferase and an RNA-methyltransferase Blair S. Nield, Robert D. Willows, Andrew E. Torda , Michael R. Gillings, Andrew J. Holmes, K. M. Helena Nevalainen, H. W. Stokes, Bridget C. Mabbutt Protein Science 13, 1651-1659 (2004) |
| 46 |
Protein Sequence Optimization - Theory, Practice, and Fundamental Impossibility Andrew E. Torda Soft Materials 2, 1-10 (2004) |
| 45 |
Sequence analysis of L RNA of Lassa virus Simon Vieth, Andrew E. Torda , Marcel Asper, Herbert Schmitz, Stephan Günther Virology 318, 153-168 (2004) |
2002 | |
| 44 |
Protein sequence threading: averaging over structures Anthony J. Russell, Andrew E. Torda Proteins: Structure, Function, and Genetics 47, 496-505 (2002) |
| 43 |
Protein structure prediction by threading: force field philosophy, approaches to alignment Thomas Huber, Andrew E. Torda -/- Editor: Igor F. Tsigelny IUL Biotechnology Series 3 (Protein Structure Prediction) 263-296 (2002), ISBN 978-0-9636817-7-5; 0-9636817-7-X |
2001 | |
| 42 |
Comparing objects of different sizes: treating proteins as strings James B. Procter, Andrew J. Perry, Andrew E. Torda Australian Journal of Chemistry 54, 367-373 (2001) |
| 41 |
Amino acid similarity matrices based on force fields Zsuzsanna Dosztányi, Andrew E. Torda Bioinformatics 17, 686-699 (2001) |
| 40 |
Free energy approximations in simple lattice proteins Dirk Reith, Thomas Huber, Florian Müller-Plathe, Andrew E. Torda Journal of Chemical Physics 114, 4998-5005 (2001) Reprint: Preprint Archive, arXiv:cond-No pp. given,mat/0008437 |
2000 | |
| 39 |
Automated protein design and sequence optimization: scoring functions and the search problem Adrian P. Cootes, Paul M. G. Curmi, Andrew E. Torda Current Protein and Peptide Science 1, 255-271 (2000) |
| 38 |
Biased Monte Carlo optimization of protein sequences Adrian P. Cootes, Paul M. G. Curmi, Andrew E. Torda Journal of Chemical Physics 113, 2489-2496 (2000) |
1999 | |
| 37 |
Sausage: protein threading with flexible force fields Thomas Huber, Anthony J. Russell, Daniel J. Ayers, Andrew E. Torda Bioinformatics 15, 1064-1065 (1999) |
| 36 |
Protein sequence threading, the alignment problem, and a two-step strategy Thomas Huber, Andrew E. Torda Journal of Computational Chemistry 20, 1455-1467 (1999) |
| 35 |
The GROMOS Biomolecular Simulation Program Package Walter R. P. Scott, Philippe H. Huenenberger, Ilario G. Tironi, Alan E. Mark, Salomon R. Billeter, Jens Fennen, Andrew E. Torda , Thomas Huber, Peter Krueger, Wilfred F. van Gunsteren Journal of Physical Chemistry A 103, 3596-3607 (1999) |
| 34 |
Enhanced protein fold recognition using secondary structure information from NMR Daniel J. Ayers, Paul R. Gooley, Asaph Widmer-Cooper, Andrew E. Torda Protein Science 8, 1127-1133 (1999) |
| 33 |
Protein fold recognition score functions: unusual construction strategies Daniel J. Ayers, Thomas Huber, Andrew E. Torda Proteins: Structure, Function, and Genetics 36, 454-461 (1999) |
1998 | |
| 32 |
Protein fold recognition without Boltzmann statistics or explicit physical basis Thomas Huber, Andrew E. Torda Protein Science 7, 142-149 (1998) |
| 31 |
The dependence of amino acid pair correlations on structural environment Adrian P. Cootes, Paul M. G. Curmi, Ross Cunningham, Christine Donnelly, Andrew E. Torda Proteins: Structure, Function, and Genetics 32, 175-189 (1998) |
1997 | |
| 30 |
Perspectives in protein-fold recognition Andrew E. Torda Current Opinion in Structural Biology 7, 200-205 (1997) |
| 29 |
Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations Alain P. Nanzer, Andrew E. Torda , Christian Bisang, Christoph Weber, John A. Robinson, Wilfred F. van Gunsteren Journal of Molecular Biology 267, 1012-1025 (1997) |
| 28 |
Structure Optimization Combining Soft-Core Interaction Functions, the Diffusion Equation Method, and Molecular Dynamics Thomas Huber, Andrew E. Torda , Wilfred F. van Gunsteren Journal of Physical Chemistry A 101, 5926-5930 (1997) |
| 27 |
Protein structure prediction force fields: parametrization with quasi-Newtonian dynamics Patrick Ulrich, Walter R. P. Scott, Wilfred F. van Gunsteren, Andrew E. Torda Proteins: Structure, Function, and Genetics 27, 367-384 (1997) |
1996 | |
| 26 |
Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach Thomas Huber, Andrew E. Torda , Wilfred F. van Gunsteren Biopolymers 39, 103-114 (1996) |
| 25 |
Molecular dynamics simulation using weak-coupling NOE distance restraining Alain P. Nanzer, Thomas Huber, Andrew E. Torda , Wilfred F. van Gunsteren Journal of Biomolecular NMR 8, 285-291 (1996) |
| 24 |
Molecular
simulation methods for generating ensembles or trajectories consistent with experimental data Wilfred F. van Gunsteren, Alain P. Nanzer, Andrew E. Torda -/- Editor: K. Binder, G. Cicotti Conference Proceedings - Italian Physical Society 49 (Monte Carlo and Molecular Dynamics of Condensed Matter Systems) 777-788 (1996) |
| 23 |
Restrained molecular dynamics of RGD-containing cyclic peptides using time-averaged NOEs A. C. Bach, S. X. Tang, J. R. Espina, Peter F. W. Stouten, William F. DeGrado, Jens Fennen, Andrew E. Torda , Alain P. Nanzer, Wilfred F. van Gunsteren Peptides: Chemistry, Structure and Biology, Proceedings of the American Peptide Symposium, 14th, Columbus, Ohio, June 18-23, 1995, 489-490 (1996) |
1995 | |
| 22 |
Structure refinement with molecular dynamics and a Boltzmann-weighted ensemble Jens Fennen, Andrew E. Torda , Wilfred F. van Gunsteren Journal of Biomolecular NMR 6, 163-170 (1995) |
| 21 |
Parametrization of time-averaged distance restraints in MD simulations Alain P. Nanzer, Wilfred F. van Gunsteren, Andrew E. Torda Journal of Biomolecular NMR 6, 313-320 (1995) |
| 20 |
Biomolecular modeling: Overview of types of methods to search and sample conformational space Wilfred F. van Gunsteren, Thomas Huber, Andrew E. Torda -/- Editor: Fernando Bernardi, Jean-Louuis Rivail AIP Conference Proceedings 330 (The first European conference on computational chemistry (E.C.C.C.1)) 253-268 (1995), ISBN 978-1-56396-457-2; 1-56396-457-0 |
1994 | |
| 19 |
Molecular mechanics in biology: from structure to function, taking account of solvation Wilfred F. van Gunsteren, F. J. Luque, David Timms, Andrew E. Torda Annual Review of Biophysics and Biomolecular Structure 23, 847-863 (1994) |
| 18 |
Reassessment of the structure of chymotrypsin inhibitor 2 (CI-2) using time-averaged NMR restraints Alain P. Nanzer, Flemming M. Poulsen, Wilfred F. van Gunsteren, Andrew E. Torda Biochemistry 33, 14503-14511 (1994) |
| 17 |
Algorithms for clustering molecular dynamics configurations Andrew E. Torda , Wilfred F. van Gunsteren Journal of Computational Chemistry 15, 1331-1340 (1994) |
| 16 |
Local elevation: a method for improving the searching properties of molecular dynamics simulation Thomas Huber, Andrew E. Torda , Wilfred F. van Gunsteren Journal of Computer-Aided Molecular Design 8, 695-708 (1994) |
| 15 |
Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and x-ray diffraction data Wilfred F. van Gunsteren, Roger M. Brunne, Piet Gros, Rene C. van Schaik, Celia A. Schiffer, Andrew E. Torda Methods in Enzymology 239 (Nuclear Magnetic Resonance, Part C) 619-654 (1994) |
1993 | |
| 14 |
Structure refinement using time-averaged J-coupling constant restraints Andrew E. Torda , Roger M. Brunne, Thomas Huber, Horst Kessler, Wilfred F. van Gunsteren Journal of Biomolecular NMR 3, 55-66 (1993) |
| 13 |
A structure refinement method based on molecular dynamics in four spatial dimensions Rene C. van Schaik, Herman J. C. Berendsen, Andrew E. Torda , Wilfred F. van Gunsteren Journal of Molecular Biology 234, 751-762 (1993) |
1992 | |
| 12 |
Molecular modeling using nuclear-magnetic-resonance data Andrew E. Torda , Wilfred F. van Gunsteren Reviews in Computational Chemistry 3, 143-172 (1992) |
1991 | |
| 11 |
The Refinement of NMR Structures by Molecular-Dynamics Simulation Andrew E. Torda , Wilfred F. van Gunsteren Computer Physics Communications 62, 289-296 (1991) |
| 10 |
On deriving spatial protein structure from NMR or x-ray diffraction data Wilfred F. van Gunsteren, Piet Gros, Andrew E. Torda , Herman J. C. Berendsen, Rene C. van Schaik Ciba Foundation Symposium 161 (Protein Conformation) 150-166 (1991) |
| 9 |
Structure determination by NMR: the modeling of NMR parameters as ensemble averages Ruud M. Scheek, Andrew E. Torda , J. Kemmink, Wilfred F. van Gunsteren NATO ASI Series, Series A: Life Sciences 225, 209-217 (1991) |
| 8 |
Time averaged distance restraints in NMR based structural refinement Andrew E. Torda , Ruud M. Scheek, Wilfred F. van Gunsteren NATO ASI Series, Series A: Life Sciences 225, 219-225 (1991) |
1990 | |
| 7 |
Time-averaged nuclear Overhauser effect distance restraints applied to tendamistat Andrew E. Torda , Ruud M. Scheek, Wilfred F. van Gunsteren Journal of Molecular Biology 214, 223-235 (1990) |
1989 | |
| 6 |
Proton NMR relaxation study of the dynamics of anthopleurin-A in solution Andrew E. Torda , Raymond S. Norton Biopolymers 28, 703-716 (1989) |
| 5 |
Time-dependent distance restraints in molecular dynamics simulations Andrew E. Torda , Ruud M. Scheek, Wilfred F. van Gunsteren Chemical Physics Letters 157, 289-294 (1989) |
1988 | |
| 4 |
Backbone folding of the polypeptide cardiac stimulant anthopleurin-A determined by nuclear magnetic resonance, distance geometry and molecular dynamics Andrew E. Torda , Bridget C. Mabbutt, Wilfred F. van Gunsteren, Raymond S. Norton FEBS Letters 239, 266-270 (1988) |
1987 | |
| 3 |
Amide proton exchange rates in cardioactive sea anemone polypeptides Andrew E. Torda , Raymond S. Norton Biochemistry International 15, 659-666 (1987) |
1985 | |
| 2 |
High-resolution proton nuclear magnetic resonance studies of human gastrin Andrew E. Torda , Graham S. Baldwin, Raymond S. Norton Biochemistry 24, 1720-1727 (1985) |
1984 | |
| 1 |
High-Resolution H1NMR Studies of Human Gastrin Andrew E. Torda , Graham S. Baldwin, Raymond S. Norton Proceedings of the Australian Biochemical Society 16, 18-18 (1984) |