BURKHARD ROST

BURKHARD ROST Email: rost@columbia.edu Phone: 212-851-4668 Location: ICRB (AUDIII - 1130 St. Nicholas Avenue) Room 805A

We try to predict aspects of protein structure and function from the evolutionary information contained in families of protein sequences. The main current projects are to (1) predict functional classes for orphans, (2) the sub-cellular localisation from sequence, and (3) protein-protein, and protein-substrate interactions from sequence and predicted structure. We also continue to work on structure prediction. Particular goals are: (1) Improve predictions for secondary structure, solvent accessibility, transmembrane proteins, (2) develop methods predicting residue-residue distances, and (3) improve methods that allow to model the 3D structure for proteins that have distant homologues of known structure (threading). Additionally, we work on describing and clustering the space of protein sequences and structures in context of structural genomics. Recently, we have analysed proteins with non- regular structures in detail.

Both in order to accomplish our goals in bioinformatics and to make our methods available, we maintain local copies of most relevant sequence databases. We also maintain a variety of servers that assist biologists in their every day sequence analysis: PredictProtein, META-PP, EVA, PredictNLS. Finally, we are working on a database that collects predictions and alignments for all entirely sequenced organisms. The technical means we apply range from scanning literature, over simple statistical methods, to methods from artificial intelligence (neural networks, hidden Markov models, or genetic algorithms).

Selected Publications

1. J Liu and B Rost (2001) Comparing function and structure between entire proteomes. Protein Science, 10, 1970-1979
2. M Cokol, R Nair and B Rost (2000) Finding nuclear localization signals. EMBO Reports, 1, 411-415
3. D Przybylski and B Rost (2001) Alignments grow, secondary structure prediction improves. Proteins, in press
4. 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
5. MA Andrade, SI O'Donoghue and B Rost (1998) Adaptation of protein surfaces to subcellular location. J of Mol Biol, 276, 517-525
6. B Rost (1998) Marrying structure and genomics. Structure, 6, 259-263
7. B Rost (1999) Twilight zone of protein sequence alignments. Protein Engineering, 12, 85-94
8. B Rost and SI O'Donoghue (1997) Sisyphus and prediction of protein structure. CABIOS, 13, 345-356
9. B Rost (1997) Protein structures sustain evolutionary drift. Folding & Design, 2, S19-S24
10. B Rost and C Sander (1993) Prediction of protein secondary structure at better than 70% accuracy. J Mol Biol, 232, 584-599