--- ------------------------------------------------------------ --- --- List of publications from CUBIC --- ------------------------------------------------------------ --- --- ------------------------------------------------------------ --- --- Papers published --- ------------------------------------------------------------ --- 1992 1. B Rost and C Sander (1992) Jury returns on structure prediction. Nature, 360, 540 2. B Rost and C Sander (1992) Exercising multi-layered networks on protein secondary structure. Neural Networks: From Biology to High Energy Physics, 3, 209-220 1993 3. T Meitinger, A Meindl, P Bork, B Rost, C Sander, M Haasemann and J Murken (1993) Molecular modelling of the Norrie disease protein predicts a cysteine knot growth factor tertiary structure. Nature Genetics, 5, 376-380 4. B Rost and G Vriend (1993) Neural networks in chemistry. CDA News, 8, 24-27 5. B Rost, C Sander and R Schneider (1993) Progress in protein structure prediction?. TIBS, 18, 120-123 6. B Rost and C Sander (1993) Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proceedings of the National Academy of Sciences, 90, 7558-7562 7. B Rost and C Sander (1993) Prediction of protein secondary structure at better than 70% accuracy. Journal of Molecular Biology, 232, 584-599 8. B Rost and C Sander (1993) Secondary structure prediction of all-helical proteins in two states. Protein Engineering, 6, 831-836 1994 9. L Holm, B Rost, C Sander, R Schneider and G Vriend (1994) Data based modeling of proteins. Statistical Mechanics, Protein Structure, and Protein Substrate Interactions, , 277-296 10. B Rost, C Sander and R Schneider (1994) PHD - an automatic server for protein secondary structure prediction. CABIOS, 10, 53-60 11. B Rost, C Sander and R Schneider (1994) Redefining the goals of protein secondary structure prediction. Journal of Molecular Biology, 235, 13-26 12. B Rost, C Sander and R Schneider (1994) Evolution and neural networks - protein secondary structure prediction above 71% accuracy. 27th Hawaii International Conference on System Sciences, 5, 385-394 13. B Rost and C Sander (1994) 1D secondary structure prediction through evolutionary profiles. in: 'Protein Structure by Distance Analysis' (eds. H Bohr and S Brunak), , 257-276 14. B Rost and C Sander (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins, 19, 55-72 15. B Rost and C Sander (1994) Conservation and prediction of solvent accessibility in protein families. Proteins, 20, 216-226 16. B Rost and C Sander (1994) Structure prediction of proteins - where are we now?. Current Opinion in Biotechnology, 5, 372-380 1995 17. B Rost and C Sander (1995) Protein structure prediction by neural networks. in: 'The handbook of brain theory and neural networks' (eds. M Arbib), , 772-775 18. B Rost and C Sander (1995) Progress of 1D protein structure prediction at last. Proteins, 23, 295-300 19. B Rost, R Casadio, P Fariselli and C Sander (1995) Prediction of helical transmembrane segments at 95% accuracy. Protein Science, 4, 521-533 20. B Rost (1995) Fitting 1-D predictions into 3-D structures. in: 'Protein folds: a distance based approach' (eds. H Bohr and S Brunak), , 132-151 21. B Rost (1995) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures. Third International Conference on Intelligent Systems for Molecular Biology, , 314-321 1996 22. T Hubbard, A Tramontano, G Barton, D Jones, M Sippl, A Valencia, A Lesk, J Moult, B Rost, C Sander, R Schneider, A Lahm, R Leplae, C Buta , M Eisenstein, O Fjellström, H Floeckner, JG Grossmann, J Hansen, M Helmer-Citterich, FS Joergensen, A Marchler-Bauer, J Osuna, J Park, A Reinhardt, L Ribas de Pouplana, A Rojo-Dominguez, V Saudek, J Sinclair, S Sturrock, C Venclovas and C Vinals (1996) Update on protein structure prediction: results of the 1995 IRBM workshop. Folding & Design, 1, R55-R63 23. B Rost (1996) NN which predicts protein secondary structure. in: 'Handbook of Neural Computation' (eds. E Fiesler and R Beale), , G4.1 24. B Rost (1996) PHD: predicting one-dimensional protein structure by profile based neural networks. Methods in Enzymology, 266, 525-539 25. B Rost and C Sander (1996) Bridging the protein sequence-structure gap by structure predictions. Annual Review of Biophysics and Biomolecular Structure, 25, 113-136 26. B Rost and A Valencia (1996) Pitfalls of protein sequence analysis. Current Opinion in Biotechnology, 7, 457-461 27. B Rost, R Casadio and P Fariselli (1996) Refining neural network predictions for helical transmembrane proteins by dynamic programming. Fourth International Conference on Intelligent Systems for Molecular Biology, , 192-200 28. B Rost, R Casadio and P Fariselli (1996) Topology prediction for helical transmembrane proteins at 86% accuracy. Protein Science, 5, 1704-1718 1997 29. B Rost, R Schneider and C Sander (1997) Protein fold recognition by prediction-based threading. Journal of Molecular Biology, 270, 471-480 30. B Rost (1997) Learning from evolution to predict protein structure. BCEC97: Bio-Computing and Emergent Computation, , 87-101 31. B Rost and SI O'Donoghue (1997) Sisyphus and prediction of protein structure. Computer Applications in Biological Science, 13, 345-356 32. B Rost (1997) Protein structures sustain evolutionary drift. Folding & Design, 2, S19-S24 33. B Rost (1997) Better 1D predictions by experts with machines. Proteins, Suppl. 1, 192-197 1998 34. MA Andrade, SI O'Donoghue and B Rost (1998) Adaptation of protein surfaces to subcellular location. Journal of Molecular Biology, 276, 517-525 35. R Zidovetzki, B Rost and I Pecht (1998) The role of transmembrane domains in the functions of B- and T-cell receptors. Immunology Letters, 64, 97-107 36. B Rost (1998) Protein structure prediction in 1D, 2D, and 3D. in: 'The Encyclopaedia of Computational Chemistry' (eds. PvR Schleyer, NL Allinger, T Clark, J Gasteiger, PA Kollman, HF Schaefer III and PR Schreiner), 3, 2242-2255 37. B Rost (1998) Marrying structure and genomics. Structure, 6, 259-263 38. B Rost (1998) Short yeast ORFs: expressed protein or not?. Protein Science, , submitted Apr 27 1999 39. A Zemla, C Venclovas, K Fidelis and B Rost (1999) A modified definition of SOV, a segment-based measure for protein secondary structure prediction assessment. Proteins, 34, 220-223 40. B Rost (1999) Twilight zone of protein sequence alignments. Protein Engineering, 12, 85-94 --- ------------------------------------------------------------ --- --- Papers pending --- ------------------------------------------------------------ --- 1. F Pazos, B Rost and A Valencia (1999) A platform for integrating threading results with other information. Bioinformatics, , in press 2. O Olmea, B Rost and A Valencia (1999) Effective use of sequence correlation and conservation in fold recognition. Journal of Molecular Biology, , in press 3. B Rost and C Sander (1999) 3rd generation prediction of secondary structure. in: 'Predicting protein structure' (eds. DM Webster), , in press 4. B Rost (1999) Evolution teaches neural networks. in: 'Scientific applications of neural nets' (eds. JW Clark, T Lindenau and ML Ristig) 5. B Rost and R Schneider (1999) Pedestrian guide to analysing sequence databases. in: 'Core techniques in biochemistry' (eds. K Ashman), , in press --- ------------------------------------------------------------ --- --- Preprints and unpublished documents --- ------------------------------------------------------------ --- 1. B Rost (1996) Protein fold recognition by merging 1D structure prediction and sequence alignments. 2. B Rost (1997) Sisyphus and protein structure prediction. 5th International Conference on Intelligent Systems for Molecular Biology, , Tutorial 3. B Rost, S O'Donoghue and C Sander (1998) Midnight zone of protein structure evolution. 4. B Rost (1999) Neural networks for protein structure prediction: hype or hit?. --- ------------------------------------------------------------ --- --- WWW published documents --- ------------------------------------------------------------ --- 1. B Rost WWW (1996) Appendix to 'Protein fold recognition by prediction-based threading'. () 2. B Rost WWW (1996) Appendix to 'Topology prediction for helical transmembrane proteins at 86% accuracy'. () 3. B Rost WWW and R Schneider (1996) WWW services for sequence analysis. (http://dodo.cpmc.columbia.edu/cubic/wwwServices/) 4. B Rost WWW (1996) Average conservation of 1D structure between remote homologues. (http://dodo.cpmc.columbia.edu/~rost/Res/96/ConservationOf1D.html) 5. B Rost WWW (1996) Observed secondary structure content for 721 proteins. (http://dodo.cpmc.columbia.edu/~rost/Res/96/SecStrContent.html) 6. B Rost WWW (1996) Accuracy of predicting buried helices by PHDsec. (http://dodo.cpmc.columbia.edu/~rost/Res/96/PredBuriedHelices.html) 7. B Rost WWW (1996) 1D structure prediction for Chameleon (IgG binding domain of protein G). (http://dodo.cpmc.columbia.edu/~rost/Res/96/PredChameleon.html) 8. B Rost WWW (1996) Expected prediction accuracy of PHD. (http://dodo.cpmc.columbia.edu/~rost/Res/96D-ExpAccuracyPHD.html) 9. B Rost WWW (1997) PredictProtein - internet prediction service. (http://dodo.cpmc.columbia.edu/predictprotein/) 10. B Rost WWW (1998) Appendix to 'Twilight zone of protein sequence alignments'. () 11. MA Andrade WWW, SI O'Donoghue and B Rost (1998) Appendix to 'Adaptation of protein surfaces to subcellular location'. (http://dodo.cpmc.columbia.edu/cubic/papers/1998_location/appendix.html)