Burkhard Rost
Address: EMBL, 69 012 Heidelberg, Germany
Correspondence: Burkhard Rost
e-mail: rost@embl-heidelberg.de
contact e-mail:rost@embl-heidelberg.de

Table of Contents

• Abstracts
• List by year
  

• List by subject:

  Secondary structure

  • Exercising Multi-layered Networks on Protein Secondary Structure
  • Prediction of protein secondary structure at better than 70% accuracy
  • Improved prediction of protein secondary structure by use of sequence profiles and neural networks
  • Secondary structure prediction of all-helical proteins in two states
  • Redefining the goals of protein secondary structure prediction
  • Combining evolutionary information and neural networks to predict protein secondary structure
  • Evolution and Neural Networks - Protein secondary structure prediction above 71% accuracy
  • 1D secondary structure prediction through evolutionary profiles
  • Progress of 1D protein structure prediction at last
  • PHD: predicting 1D protein structure by profile based neural networks
  • Better 1D predictions by experts with machines

    Solvent accessibility

  • Conservation and prediction of solvent accessibility in protein families
  • PHD: predicting 1D protein structure by profile based neural networks
  • Better 1D predictions by experts with machines

    Transmembrane segments

  • Prediction of helical transmembrane segments at 95% accuracy
  • PHD: predicting 1D protein structure by profile based neural networks
  • Refining neural network predictions for helical transmembrane proteins by dynamic programming
  • Topology prediction for helical transmembrane proteins at 86% accuracy

    Threading

  • Fitting 1D predictions into 3D structures
  • TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures
  • Protein fold recognition by prediction-based threading

    Evolution

  • Protein structures evolve at random - almost
  • Protein structures sustain evolutionary drift
  • Twilight zone of protein sequence alignments

    Function

  • Adaptation of protein surfaces to subcellular location

    Prediction services

  • PHD - an automatic server for protein secondary structure prediction
  • Pedestrian guide to analysing sequence database
  • Progress of 1D protein structure prediction at last
  • PHD: predicting 1D protein structure by profile based neural networks
  • Better 1D predictions by experts with machines
  • Pitfalls of protein sequence analysis

    Reviews

  • Neural Networks in Chemistry
  • Progress in protein structure prediction?
  • Structure prediction of proteins - where are we now?
  • Protein Structure Prediction by Neural Networks
  • Bridging the protein sequence-structure gap by predictions?
  • NN which predicts protein secondary structure
  • Pitfalls of protein sequence analysis
  • PHD: predicting 1D protein structure by profile based neural networks
  • Sisyphus and protein structure prediction
  • Protein structure prediction in 1D, 2D, and 3D
  • Learning From Evolution To Predict Protein Structure
  • 3rd Generation Prediction Of Secondary
  • Marrying structure and genomics

1992
1. B. Rost and C. Sander, Exercising Multi-layered Networks on Protein Secondary Structure, in: O. Benhar, S. Brunak, P. DelGiudice and M. Grandolfo (eds.), Neural Networks: From Biology to High Energy Physics, Elba, Italy: International Journal of Neural Systems, 209-220 (1992).
2. B. Rost and C. Sander, Jury returns on structure prediction, Nature, 360, 540 (1992).

   1993

3. B. Rost and C. Sander, Improved prediction of protein secondary structure by use of sequence profiles and neural networks, Proceedings of the National Academy of Sciences, 90, 7558-7562 (1993).
4. B. Rost and C. Sander, Secondary structure prediction of all-helical proteins in two states, Prot. Engin., 6, 831-836 (1993).
5. B. Rost and C. Sander, Prediction of protein secondary structure at better than 70% accuracy, J. Mol. Biol., 232, 584-599 (1993).
6. B. Rost, C. Sander and R. Schneider, Progress in protein structure prediction?, TIBS, 18, 120-123 (1993).
7. B. Rost and G. Vriend, Neural Networks in Chemistry, CDA News, 8, 24-27 (1993).
8. T. Meitinger, A. Meindl, P. Bork, B. Rost, C. Sander, M. Haasemann and J. Murken, Molecular modelling of the Norrie disease protein predicts a cyste knot growth factor tertiary structure, Nature Genetics, 5, 376-380 (1993).

   1994

9. B. Rost and C. Sander, 1D secondary structure prediction through evolutionary profiles, in: H. Bohr and S. Brunak (eds.), Protein Structure by Distance Analysis, Amsterdam, Oxford, Washington: IOS Press, 257-276 (1994).
10. B. Rost and C. Sander, Combining evolutionary information and neural networks to predict protein secondary structure, Proteins, 19, 55-72 (1994).
11. B. Rost and C. Sander, Conservation and prediction of solvent accessibility in protein families, Proteins, 20, 216-226 (1994).
12. B. Rost and C. Sander, Structure prediction of proteins - where are we now?, Cur. Opin. Biotech., 5, 372-380 (1994).
13. B. Rost, C. Sander and R. Schneider, Redefining the goals of protein secondary structure prediction, J. Mol. Biol., 235, 13-26 (1994).
14. B. Rost, C. Sander and R. Schneider, PHD - an automatic server for protein secondary structure prediction, CABIOS, 10, 53-60 (1994).
15. B. Rost, C. Sander and R. Schneider, Evolution and Neural Networks - Protein secondary structure prediction above 71% accuracy, in: L. Hunter (eds.), 27th Hawaii International Conference on System Sciences, Wailea, Hawaii, U.S.A.: IEEE Society Press, 385-394 (1994).
16. L. Holm, B. Rost, C. Sander, R. Schneider and G. Vriend, Data based modeling of proteins, in: S. Doniach (eds.), Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, New York: Plenum Press, 277-296 (1994).

    1995

17. B. Rost, Fitting 1D predictions into 3D structures, in: H. Bohr and S. Brunak (eds.), Protein folds: a distance based approach, Boca Raton, Florida: CRC Press, 132-151 (1995).
18. B. Rost, TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures, in: C. Rawlings, D. Clark, R. Altman, L. Hunter, T. Lengauer and S. Wodak (eds.), Third International Conference on Intelligent Systems for Molecular Biology, Cambridge, England: AAAI Press, 314-321 (1995).
19. B. Rost, R. Casadio, P. Fariselli and C. Sander, Prediction of helical transmembrane segments at 95% accuracy, Prot. Science, 4, 521-533 (1995).
20. B. Rost and C. Sander, Protein Structure Prediction by Neural Networks, in: M. Arbib (eds.), The Handbook of Brain Theory and Neural Networks, Cambridge, MA: Bradford Books/The MIT Press, 772-775 (1995).
21. B. Rost and C. Sander, Progress of 1D protein structure prediction at last, Proteins, 23, 295-300 (1995).
22. B. Rost and C. Sander, Pitfalls in analysing protein sequences: some salutary lessons, EMBL Heidelberg, Germany (1995).
23. S. é. O'Donoghue and B. Rost, Computational tools for experimental determination and theoretical prediction of protein structure, EMBL Heidelberg, Germany (1995).

    1996

24. B. Rost, PHD: predicting one-dimensional protein structure by profile based neural networks, Meth. Enzymol., 266, 525-539 (1996).
25. B. Rost, R. Casadio and P. Fariselli, Refining neural network predictions for helical transmembrane proteins by dynamic programming, in: D. States, P. Agarwal, T. Gaasterland, L. Hunter and R. F. Smith (eds.), Fourth International Conference on Intelligent Systems for Molecular Biology, St. Louis, M.O., U.S.A.: Menlo Park, CA: AAAI Press, 192-200 (1996).
26. B. Rost, R. Casadio and P. Fariselli, Topology prediction for helical transmembrane proteins at 86% accuracy, Prot. Science, 5, 1704-1718 (1996).
27. B. Rost and C. Sander, Bridging the protein sequence-structure gap by predictions?, Ann. Rev. Biophys. Biomol. Struc., 25, 113-136 (1996).
28. B. Rost and A. Valencia, Pitfalls of protein sequence analysis, Cur. Opin. Biotechn., 7, 457-461 (1996).
29. B. Rost, NN which predicts protein secondary structure, in: E. Fiesler and R. Beale (eds.), Handbook of Neural Computation, New York: Oxford Univ. Press, G4.1 (1996).
30. B. Rost T, Sneaking in genomes for helical transmembrane proteins, EMBL, Heidelberg, Germany (1996).
31. B. Rost WWW, Observed secondary structure content for 721 proteins, EMBL Heidelberg, Germany (1996).
32. B. Rost WWW, Average conservation of 1D structure between remote homologues, EMBL Heidelberg, Germany (1996).
33. B. Rost WWW, Appendix to `Topology prediction for helical transmembrane proteins at 86% accuracy', EMBL (1996).
34. B. Rost WWW, Prediction of topology for all helical transmembrane proteins of Haemophilus influenzae, EMBL (1996).
35. B. Rost WWW, 1D structure prediction for Chameleon (IgG binding domain of protein G), EMBL Heidelberg, Germany (1996).
36. B. Rost WWW, Appendix to `Protein fold recognition by prediction-based threading', EMBL (1996).
37. B. Rost WWW, Protein fold recognition by merging 1D structure prediction and sequence alignments, EMBL Heidelberg, Germany (1996).
38. B. Rost WWW, Expected prediction accuracy of PHD, EMBL Heidelberg, Germany (1996).
39. B. Rost WWW, Accuracy of predicting buried helices by PHDsec, EMBL Heidelberg, Germany (1996).
40. B. Rost WWW, S. O'Donoghue and C. Sander, Protein structures evolve at random - almost, EMBL (1996).
41. B. Rost WWW and R. Schneider, WWW services for sequence analysis, EMBL (1996).
42. T. Hubbard, et al., Update on protein structure prediction: results of the 1995 IRBM workshop, Folding & Design, 1, R55-R63 (1996).

    1997

43. B. Rost, Protein structures sustain evolutionary drift, Folding & Design, 2, 519-524 (1997).
44. B. Rost, R. Schneider and C. Sander, Protein fold recognition by prediction-based threading, J. Mol. Biol., 270, 471-480 (1997).
45. B. Rost and S. I. O'Donoghue, Sisyphus and prediction of protein structure, CABIOS, 13, 345-356 (1997).
46. B. Rost WWW, PredictProtein - internet prediction service, EMBL (1997).

47. B. Rost, Learning from evolution to predict protein structure, in: B. Olsson, D. Lundh and A. Narayanan (eds.), BCEC97: Bio-Computing and Emergent Computation, Skövde, Sweden, Sep 1-2, 1997. World Scientific, 87 - 101 (1997).

    1998

48. B. Rost, Better 1D predictions by experts with machines, Proteins, Suppl. 1, 192-197 (1998).
49. M. Andrade, S. I. O'Donoghue and B. Rost, Adaptation of protein surfaces to subcellular location, J. Mol. Biol., 276, 517-525 (1998).
50. B. Rost, Marrying structure and genomics, Structure, 6, 259-263 (1998).
51. B. Rost, Protein structure prediction in 1D, 2D, and 3D, in: P. von Ragué Schleyer, N. L. Allinger, T. Clark, J. Gasteiger, P. A. Kollman and H. F. I. Schaefer (eds.), Encyclopedia of computational chemistry, Sussex: John Wiley & Sons, in press (1998).
52. C. Perez-Iratxeta, B. Rost and A. Valencia, Variety of functions performed by proteins of similar structures, J. Mol. Evol., submitted (1998).
53. B. Rost, S. O'Donoghue and C. Sander, Midnight zone of protein structure evolution, manuscript in preparation (1998).

    1999

54. B. Rost, Twilight zone of protein sequence alignments, Protein Engineering, 12, 85-94 (1999).
    pending:
    
55. B. Rost and R. Schneider, Pedestrian guide to analysing sequence databases, in: K. Ashman (eds.), Core techniques in biochemistry, Heidelberg: Springer, in press (1999).
56. B. Rost and C. Sander, 3rd Generation Prediction Of Secondary, in: D. W. Webster (ed.) Predicting protein structure'. Humana Press, in press (1999)