Burkhard Rost

Department of Biochemistry and Molecular Biophysics since 1998

Theoretical physicist trapped in molecular biology by the bright colours of life

• Note: the latest version of papers, results, talks may be at CUBIC
• Programs and Results
  • Available programs and services
  • Predictions of transmembrane helices for entire genomes
  • Other (un)published results and WWW material
• Publications
  • List of publications in molecular biology (sorted by year, sorted by subject)
  • Appendices to publications and WWW material
  • WWW versions of papers published
  • Excerpts from talks
• Projects
• Goals
• WWW services for molecular biology (commented hotlist)
• Address(es)

Slow connection? download all files from my home directory! (How to use your local version?)

Software services:

• PredictProtein:
  Automatic service (email or WWW) for: sequence alignment; prediction of secondary structure; prediction of residue solvent accessibility; prediction of transmembrane helix locations; prediction of topology for helical transmembrane proteins; prediction-based threading (alignment of remote homologues); and evaluation of secondary structure prediction methods
• Catalogue of software

Projects:

• Neural networks applications to 'real life' problems
• Prediction of aspects of protein structure (secondary structur: PHDsec, solvent accessibility: PHDacc, helical transmembrane segments: PHDhtm)
• Yet another way of threading sequences into known 3D structures (TOPITS)
• Prediction of binding sites
• Prediction of inter-residue contacts
• Prediction of the subcellular localisation of proteins
• Prediction of function and functional class
• Evaluation of protein secondary structure predictions (EvalSec)
• Evaluation of alignment accuracy, in general, and of threading experiments, in particular (AQUA, NOTE: put on hold for time being ...)
• Simplification of WWW services for molecular biologists (PredictProtein)

Goals:

• Short run: Automatical ab initio prediction of protein 3D structure
• Middle run: Automatical ab initio prediction of protein function
• Long run: Stepping up in complexity: intruding into to complex cellular processes by theoretical means

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                                             New York, USA
                                             -------------
         Burkhard Rost 
* off    CUBIC, Columbia University
         Department of Biochemistry & Molecular Biophysics
         630 West, 168 Street
         New York, N.Y. 10032
  tel    +1-212-305 3773
         +1-212-305 3882 (Department)
         +1-212-305 3283 (Katie Rosa)
  fax    +1-212-305 7932

* priv   +1-212-665 5099
                                       Heidelberg, Germany
                                       -------------------
* priv   Wilckens 15, 69120 Heidelberg
  tel    +49-(0)6221-410402

*        LION Bioscience 
         Im Neuenheimer Feld 515-517, 69120 Heidelberg
  tel    +49-(0)6221-4038-0
  fax    +49-(0)6221-4038-101

*        EMBL (European Molecular Biology Laboratory)
         69012 Heidelberg
  fax    +49-(0)6221-387 517
  tel    +49-(0)6221-387 305

email   rost@columbia.edu        
        rost@dodo.cpmc.columbia.edu        
        rost@EMBL-Heidelberg.DE        
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Last updated: Dec 22, 1999