Andrew Torda Publications

Margraf, T., Schenk, G. and Torda, A.E. (2009) Nucleic Acids Res. doi: 10.1093/nar/gkp431. The SALAMI protein structure search server.

Kong, S-G., Fan, W-L., Chen, H-D., Wigger, J., Torda, A.E. and Lee, H.C. (2009) Phys. Rev. E, doi:10.1103, Phys Rev E 79.061911 A quantitative measure of randomness and order for complete genomes.

Schenk, G., Margraf, T., Torda, A.E. (2008) Algo. Mol. Biol. 3, doi:10.1186. Protein sequence and structure alignments within one framework.

Nguyen, P.H., Mittag, E., Torda, A.E. and Stock, G.(2006) J. Chem. Phys 124, 154107. Improved Wang-Landau sampling through the use of smoothed potential energy surfaces.

Jordanova, R., Radoslavov, G., Fischer, P., Torda, A.E., Lottspeich, F., Boteva, R., Walter, R.D., Bankov, I. and Liebau, E. (2005) J. Biol. Chem. 380, 41429-41438. The highly abundant protein Ag-lbp55 from Ascaridia galli represents a novel type of lipid binding protein.

Torda, A.E. (2005) in The Proteomics Handbook (Ed. Walker, J.M.) Humana Press, Totowa N.J. pp 921-938, Protein Threading.

Kühnl, J, Bobik, T, Procter, J.B., Burmeister, Höppner, J., Wilde, I., Lüersen, K., Torda, A.E., Walter, R.D., Liebau, E. (2005) FEBS J., 272, 1465-1477. The methylmalonyl-CoA epimerase from Caenorhabditis elegans.

Torda, A.E., Procter, J.B. and Huber, T. (2004) Nucleic Acids Res. 32, W532-W535. WURST: A protein threading server with a structural scoring function, sequence profiles and optimised substitution matrices.

Nield, B.S., Willows, R.D., Torda, A.E., Gillings, M.R., Holmes, A.J., Nevalainen, K.M.H., Stokes, H.W. and Mabbutt, B.M. (2004) Protein Sci. 13, 1651-1659. New enzymes from environmental cassette arrays: Functional attributes of a phosphotransferase and a RNA-methyltransferase.

Torda, A.E. (2004) Soft Materials, 2, 1-10. Protein sequence optimisation - theory, practice and fundamental impossibility.

Vieth, S., Torda, A.E., Asper, M., Schmitz, H. and Günther, S. (2004) Virology, 318, 153-168. Sequence Analysis of L RNA of Lassa virus.

Huber, T. and Torda, A.E. (2002) in Protein Structure Prediction: A Bioinformatic Approach (Ed. Tsigelny, I.) International University Line, La Jolla U.S.A. Protein structure prediction by threading: force field philosophy, approaches to alignment.

Russell, A.J. and Torda, A.E. (2002) Proteins, 47, 496-505. Protein sequence threading - averaging over structures.

Dosztanyi, Zs. and Torda, A.E. (2001) Bioinformatics, 17, 686-699. Amino acid similarity matrices based on force fields.

Procter, J.B., Perry, A.J. and Torda, A.E. (2001) Aust. J. Chem., 54. 367-373. Comparing objects of different sizes: treating proteins as strings.

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

Cootes, A.P., Curmi, P.M.G., Torda, A.E. (2000) Curr. Prot. Pept. Sci., 3, 255-271. Automated Protein Design and Sequence Optimisation: Scoring Functions and the Search Problem.

Cootes, A.P., Curmi, P.M.G., Torda, A.E. (2000) J. Chem. Phys. 113, 2849-2496. Biased Monte Carlo Optimisation Of Protein Sequences

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

Ayers, D.J., Huber, T., Torda, A.E. (1999) Proteins, 36, 454-461. Protein fold recognition score functions: unusual construction strategies.

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

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

Ayers, D.J., Gooley, P.R., Widmer-Cooper, A., Torda, A.E. (1999) Protein Sci., 8, 1127-1133. Enhanced protein fold recognition using secondary structure information from NMR.

Cootes, A.P., Curmi, P.M.G., Cunningham, R., Donnelly, C., Torda, A.E. (1998) Proteins. 32, 175-179. The dependence of amino acid pair correlations on structural environment.

Huber, T., Torda, A.E. (1998) Protein Sci. 7, 142-149. Protein Fold Recognition Without Boltzmann Statistics or Explicit Physical Basis

Torda, A.E. (1997) Curr. Opin. Struct. Biol., 7, 200-205. Perspectives on Protein Fold Recognition

Ulrich, P., Scott, W., van Gunsteren, W.F., Torda, A.E. (1997) Proteins, 27, 367-384. Protein structure prediction force fields: Parametrization with quasi-Newtonian dynamics.

Huber, T., Torda, A.E., van Gunsteren, W.F. (1997) J. Phys. Chem. A 101, 5926-5930. Structure Optimisation Combining Soft-Core Interaction Functions, the Diffusion Equation Method and Molecular Dynamics.

Nanzer, A.P., Torda, A.E., Bisang, C., Weber, C., Robinson, J.A., van Gunsteren, W.F. (1997) J. Mol. Biol., 267, 1011-1024. Dynamical Studies of Peptide Motifs in the Plasmodium falciparum Circumsporozoite Surface Protein by Restrained and Unrestrained MD Simulations.

Torda, A.E. (1997) Trends in Biotech., 15, 380-381. Guessing protein structures.

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

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

van Gunsteren, W.F., Nanzer, A.P., Torda, A.E. (1996) in Monte Carlo and Molecular Dynamics of Condensed Matter, (Eds Binder, K. and Cicotti, G.) Conf Proc vol. 49, Ital. Phys. Soc. Bologna.

Schwarz, B.M., Torda, A.E. (1996) CD liner notes translation for Pallinckx, Live At the Border, Intakt, CD047, Zürich.

Nanzer, A.P., van Gunsteren, W.F., Torda (1995) J. Biomol. NMR, 6, 313-320. Parametrisation of time-averaged distance restraints in MD simulations.

van Gunsteren, W.F., Huber, T., Torda, A.E. (1995) Conference Proc No. 330: European Conference on Computational Chemistry (Eds Bernardi, F. and Rivail, J-L) pp 263-268, Am. Inst. Physics, New York. Biomolecular modelling: overview of methods to search and sample conformational space.

Fennen, J., Torda, A.E., van Gunsteren, W.F. (1995) J. Biomol. NMR, 6, 163-170. Structure Refinement with Molecular Dynamics and a Boltzmann weighted Ensemble.

Nanzer, A.P., Poulsen, F.M., van Gunsteren, W.F., Torda, A.E. (1994) Biochemistry, 33, 14503-14511. A reassessment of the structure of Chymotrypsin Inhibitor 2 (CI-2) using time averaged NMR restraints.

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

Torda, A.E., van Gunsteren, W.F. (1994) J. Comput. Chem., 15, 1331-1340. Algorithms for clustering molecular dynamics configurations.

van Gunsteren, W.F., Luque, F.J., Timms, D., Torda, A.E. (1994) Ann. Rev. Biophys. Biomol. Struct., 23, 847-863. Molecular mechanics in biology: From structure to function, taking account of solvation.

van Gunsteren, W.F., Brunne, R.M., Gros, P., van Schaik, R.C., Schiffer, C.A., Torda, A.E. (1994) Methods In Enzymology, 239, 619-654. Accounting for molecular mobility in structure determination based on NMR spectroscopic and X-ray diffraction data.

van Schaik, R.C., Berendsen, H.J.C., Torda, A.E., van Gunsteren, W.F. (1993) J. Mol. Biol., 234, 751-762. A structure refinement method based on molecular dynamics in 4 spatial Dimensions.

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

Torda, A.E., van Gunsteren, W.F. (1992) In Reviews in Computational Chemistry (Eds. Lipkowitz, K.B. Boyd, D.B.) VCH Publishers, Boston. Molecular modelling using NMR data.

Scheek, R.M., Torda, A.E., Kemminck, J., van Gunsteren, W.F. (1991) In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (Eds. Hoch, J.C., Poulsen, F.M and Redfield, C.) 209-218. Structure Determination by NMR: The Modeling of NMR Parameters as Ensemble Averages.

Torda, A.E., Scheek, R.M., van Gunsteren, (1991) In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (Eds. Hoch, J.C., Poulsen, F.M and Redfield, C.) pp 219-226. Time Averaged Distance Restraints in NMR Based Structural Refinement.

van Gunsteren, W.F., Gros, P., Torda, A.E., Berendsen, H.J.C., van Schaik, R.C. (1991) In Protein Conformation (Eds. Chadwick, D.J. and Widdows, K.) Wiley-Interscience, Ciba Foundation Symposium 161, 150-166. On deriving spatial structure from NMR or X-ray diffraction data.

Torda, A.E., van Gunsteren, W.F. (1991) Computer Phys. Comm., 62, 289-296. The Refinement of NMR structures by Molecular Dynamics Simulation.

Torda, A.E., Scheek, R.M., van Gunsteren, W.F. (1990) J. Mol. Biol., 214, 223-235. Time-averaged Nuclear Overhauser Effect Distance Restraints Applied to Tendamistat.

Torda, A.E., Scheek, R.M., van Gunsteren, W.F. (1989) Chem. Phys. Lett., 157, 289-294. Time-dependent distance restraints in molecular dynamics simulations.

Torda, A.E., Norton, R.S. (1989) Biopolymers,28, 703-716. Proton NMR relaxation study of Anthopleurin-A in solution.

Torda, A.E., Mabbutt, B.C., van Gunsteren, W.F., Norton, R.S. (1988) FEBS Lett., 239, 266-270. Backbone folding of the polypeptide cardiac stimulant anthopleurin-A determined by nuclear magnetic resonance, distance geometry and molecular dynamics.

Torda, A.E., Norton, R.S.(1987) Biochem. Intl., 15, 659-666. Amide proton exchange rates in cardioactive sea anemone polypeptides.

Torda, A.E., Baldwin, G.S., Norton, R.S. (1985) Biochemistry, 24, 1720-1727. High resolution ¹H NMR studies of the human polypeptide hormone gastrin.

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Last revised 24 Aug 2006