Zentrum für Bioinformatik
Telefon: +49 (40) 42838 7331
eMail: torda (at) zbh.uni-hamburg.de
- Low resolution force fields for protein structure prediction / protein threading
- Abuse of force fields - turning them into substitution matrices, building ones for special problems
- Scoring functions and methodology for optimising protein sequences
- Model systems on lattices for problems like free energy estimation and sequence optimisation
- Methods for protein sequence to structure alignment
There is some documentation for the most recent code that you might like to read.
Protein Structure Prediction
Our favourite threading code travels under the name of wurst. You can read some documentation. Our web server is running and does threading using a mixture of sequence terms and a structural term based on Bayesian classification of fragment properties.
We have been optimising amino acid substitution matrices for protein sequence alignments. Some people have asked for copies, so I have gathered three of them together. Please do tell me if they turn out to be useful to you.
I worked in the Netherlands from 1988 until 1990 and then at the ETH in Zuerich for 5 years. In 1995, I became a group leader in the Research School of Chemistry at the Australian National University. I moved to Hamburg in October 2002.
Why not have a look at the pages of the group members? They do the real work and have better photos than me.
Is collected here.
We have collected a list of software projects. This might be of interest for people from the other year who were wondering about the kind of things that we do in our group.
and some very old ones
Here is our (mine and Jan Wigger's) code for simulating genome growth.
Sorry, but this is prone to abuse, so you will have to type it yourself. Put "torda" before @zbh.uni-hamburg.de.