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Andrew Torda: Publikationen

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Journalveröffentlichungen

43.	Wigger, J., Kong, S-G., Chen, H-D., Fan, W-L., Lee, H. C., Torda, A.E. (2007). Numerical models for genome growth. Bioinformatics, submitted.
42.	Nguyen, P.H., Mittag, E., Torda, A.E., Stock, G. (2006). Improved Wang-Landau sampling through the use of a generalised effective potential. Journal of Chemical Physics, 124:154107. Reprint anfordern →
41.	Jordanova, R., Radoslavov, G., Fischer, P., Torda, A. E., Lottspeich, F., Boteva, R., Walter, R. D., Bankov, I., Liebau, E. (2005). The highly abundant protein Ag-Ibp55 from Ascaridia galli represents a novel type of lipid-binding proteins. Journal of Biological Chemistry, 280:41429-41438. Reprint anfordern →
40.	Kühnl, J., Bobik, T., Procter, J. B., Burmeister, C., Höppner, J., Wilde, I., Lüersen, K., Torda, A. E., Walter, R. D., Liebau, E. (2005). The methylmalonyl-CoA epimerase from Caenorhabditis elegans. FEBS Journal, 272:1465-1477. Reprint anfordern →
39.	Vieth, S., Torda, A. E., Asper, M., Schmitz, H., Günther, S. (2004). Sequence analysis of L RNA of Lassa virus. Virology, 318:153-168. Reprint anfordern →
38.	Torda, A. E. (2004). Protein sequence optimization - theory, practice and fundamental impossibility. Soft Materials, 2:1-10. Reprint anfordern →
37.	Torda, A. E., Procter, J. B., Huber, T. (2004). Wurst: A protein threading server with a structural scoring function, sequence profiles and optimised substitution matrices. Nucleic Acids Research, 32:W532-W535. Reprint anfordern →
36.	Russell, A, Torda, A. E. (2002). Protein sequence threading - averaging over structures. Proteins: Structure Function and Genetics, 47:496-505. Reprint anfordern →
35.	Reith, D., Huber, T., Müller-Plathe, F., Torda, A. E. (2001). Free energy approximations in simple lattice proteins. Journal of Chemical Physics, 114:4998-5005. Reprint anfordern →
34.	Procter, J, B, Perry, A.J., Torda, A.E. (2001). Comparing objects of different sizes: treating proteins as strings. Australian Journal of Chemistry, 54:367-374. Reprint anfordern →
33.	Dosztányi, Zs, Torda, A. E. (2001). Amino acid substitution matrices based on force fields. Bioinformatics, 17:686-699. Reprint anfordern →
32.	Cootes, A. P., Curmi, P. M. G., Torda, A. E. (2000). Biased Monte Carlo optimization of protein sequences. Journal of Chemical Physics, 113:2489-2496. Reprint anfordern →
31.	Ayers, D. J., Huber, T., Torda, A. E. (1999). Protein fold recognition score functions: unusual construction strategies. Proteins, 36:454-461. Reprint anfordern →
30.	Huber, T., Russell, A.J., Ayers, D., Torda, A.E. (1999). SAUSAGE: Protein threading with flexible force fields. Bioinformatics, 15:1064-1065. Reprint anfordern →
29.	Ayers, D.J., Gooley, P.R., Widmer-Cooper, A., Torda, A.E. (1999). Enhanced protein fold recognition using secondary structure information from NMR. Protein Science, 8:1127-1133. Reprint anfordern →
28.	Huber, T., Torda, A.E. (1999). Protein sequence threading, the alignment problem and a two step strategy. Journal of Computational Chemistry, 20:1455-1467. Reprint anfordern →
27.	Scott, W. R. P., Hunenberger, P. H., Tironi, I. G., Mark, A. E., Billeter, S. R., Fennen, J., Torda, A. E., Huber, T., Kruger, P., van Gunsteren, W. F. (1999). The GROMOS biomolecular simulation program package. Journal of Physical Chemistry A, 103:3596-3607. Reprint anfordern →
26.	Cootes, A. P., Curmi, P. M. G., Cunningham, R., Donnelly, C., Torda, A. E. (1998). The dependence of amino acid pair correlations on structural environment. Proteins-Structure Function and Bioinformatics, 32:175-189. Reprint anfordern →
25.	Huber, T., Torda, A. E. (1998). Protein Fold Recognition Without Boltzmann Statistics or Explicit Physical Basis. Protein Science, 7:142-149. Reprint anfordern →
24.	Torda, A. E. (1997). Perspectives in protein-fold recognition. Curr Opin Struct Biol, 7:200-5. Reprint anfordern →
23.	Ulrich, P., Scott, W., van Gunsteren, W.F., Torda, A. E. (1997). Protein Structure Prediction Force Fields - Parametrization With Quasi-Newtonian Dynamics. Proteins, 27:367-384. Reprint anfordern →
22.	Nanzer, A. P., Torda, A. E., Bisang, C., Weber, C., Robinson, J. A., van Gunsteren, W. F. (1997). Dynamical studies of peptide motifs in the Plasmodium falciparum circumsporozoite surface protein by restrained and unrestrained MD simulations. Journal of Molecular Biology, 267:1012-1025. Reprint anfordern →
21.	Huber, T., Torda, A. E., van Gunsteren, W. F. (1997). Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics. Journal of Physical Chemistry A, 101:5926-5930. Reprint anfordern →
20.	Nanzer, A. P., Huber, T., Torda, A. E., van Gunsteren, W. F. (1996). Molecular dynamics simulation using weak-coupling NOE distance restraining. Journal of Biomolecular NMR, 8:285-291. Reprint anfordern →
19.	Huber, T., Torda, A. E., van Gunsteren, W. F. (1996). Optimization methods for conformational sampling using a Boltzmann-weighted mean field approach. Biopolymers, 39:103-114. Reprint anfordern →
18.	Fennen, J., Torda, A. E., van Gunsteren, W. F. (1995). Structure Refinement with Molecular-Dynamics and a Boltmann-Weighted Ensemble. Journal of Biomolecular NMR, 6:163-170. Reprint anfordern →
17.	Nanzer, A. P., van Gunsteren, W. F., Torda, A. E. (1995). Parametrization of Time-Averaged Distance Restraints in MD Simulations. Journal of Biomolecular NMR, 6:313-320. Reprint anfordern →
16.	van Gunsteren, W. F., Luque, F. J., Timms, D., Torda, A. E. (1994). Molecular Mechanics in Biology - from Structure to Function, Taking Account of Solvation. Annual Review of Biophysics and Biomolecular Structure, 23:847-863. Reprint anfordern →
15.	Torda, A. E., van Gunsteren, W. F. (1994). Algorithms for Clustering Molecular-Dynamics Configurations. Journal of Computational Chemistry, 15:1331-1340. Reprint anfordern →
14.	Nanzer, A. P., Poulsen, F. M., van Gunsteren, W. F., Torda, A. E. (1994). A Reassessment of the Structure of Chymotrypsin Inhibitor-2 (Ci-2) Using Time-Averaged NMR Restraints. Biochemistry, 33:14503-14511. Reprint anfordern →
13.	Huber, T., Torda, A. E., van Gunsteren, W. F. (1994). Local Elevation - a Method for Improving the Searching Properties of Molecular-Dynamics Simulation. Journal of Computer-Aided Molecular Design, 8:695-708. Reprint anfordern →
12.	van Gunsteren, W. F., Brunne, R. M., Gros, P., van Schaik, R. C., Schiffer, C. A., Torda, A. E. (1994). Accounting for molecular mobility in structure determination based on nuclear magnetic resonance spectroscopic and X-ray diffraction data. Methods Enzymol, 239:619-54..
11.	Torda, A. E., Brunne, R. M., Huber, T., Kessler, H., van Gunsteren, W. F. (1993). Structure Refinement Using Time-Averaged J-Coupling Constant Restraints. Journal of Biomolecular NMR, 3:55-66. Reprint anfordern →
10.	van Schaik, R. C., Berendsen, H. J. C., Torda, A. E., van Gunsteren, W. F. (1993). A Structure Refinement Method Based on Molecular-Dynamics in 4 Spatial Dimensions. Journal of Molecular Biology, 234:751-762. Reprint anfordern →
9.	Torda, A. E., van Gunsteren, W. F. (1991). The Refinement of NMR Structures by Molecular-Dynamics Simulation. Computer Physics Communications, 62:289-296. Reprint anfordern →
8.	van Gunsteren, W. F., Gros, P., Torda, A. E., Berendsen, H. J. C., van Schaik, R. C. (1991). On Deriving Spatial Protein-Structure from NMR or X-Ray-Diffraction Data. Ciba Foundation Symposia, 161:150-166.
7.	Torda, A. E., Scheek, R.M., van Gunsteren, W. F. (1990). Time-averaged nuclear overhauser effect distance restraints applied to tendamistat. J Mol Biol, 214:223-235. Reprint anfordern →
6.	Torda, A. E., Norton, R. S. (1989). Proton NMR Relaxation Study of the Dynamics of Anthopleurin-a in Solution. Biopolymers, 28:703-716. Reprint anfordern →
5.	Torda, A. E., Scheek, R. M., van Gunsteren, W. F. (1989). Time-Dependent Distance Restraints in Molecular-Dynamics Simulations. Chemical Physics Letters, 157:289-294. Reprint anfordern →
4.	Torda, A. E., Mabbutt, B. C., van Gunsteren, W. F., Norton, R. S. (1988). Backbone Folding of the Polypeptide Cardiac Stimulant Anthopleurin-a Determined by Nuclear Magnetic-Resonance, Distance Geometry and Molecular-Dynamics. Febs Letters, 239:266-270. Reprint anfordern →
3.	Torda, A. E., Norton, R. S. (1987). Amide Proton-Exchange Rates in Cardioactive Sea-Anemone Polypeptides. Biochemistry International, 15:659-666.
2.	Torda, A. E., Baldwin, G. S., Norton, R. S. (1985). High-Resolution Proton Nuclear Magnetic-Resonance Studies of Human Gastrin. Biochemistry, 24:1720-1727. Reprint anfordern →
1.	Torda, A. E., Baldwin, G. S., Norton, R. S. (1984). High-Resolution H¹NMR Studies of Human Gastrin. Proceedings of the Australian Biochemical Society, 16:18-18.

Buchkapitel

3.	Torda, A. E. (2005). Protein Threading. In The Proteomics Protocols Handbook (Walker, J. M., ed.). Humana Press. Reprint anfordern →
2.	Huber, T., Torda, A. E. (2002). Protein structure prediction by threading: force field philosophy, approaches to alignment.. In Protein structure prediction: A bioinformatic approach (Tsigelny, I. F., ed.), pp. 263-298. International University Line. Reprint anfordern →
1.	Torda, A. E., van Gunsteren, W. F. (1992). Molecular modeling using nuclear magnetic resonance. In Reviews in computational chemistry III (Lipkowitz, KB, Boyd, DB, Boyd, DB, ed.), Vol. III, pp. 143-172. VCH.

Impressum

Letzte Aktualisierung: 2009-04-09