Prof. Dr. Andrew Torda

• 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

You will get a better idea if you look at my list of publications. 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.

Substitution Matrices

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.

• Iryna Bondarenko
• Björn Hansen
• Marco Matthies
• Martin Mosisch
• Annette Schade

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.

• Tuesday 26 Feb 2008, Hamburg, Uni Klinik Eppendorf, Some group activities
• Tuesday 19 Feb 2008, Bled, Slovenia, RNA base pairing prediction using self consistent mean field theory

and some very old ones

• Wednesday 14 Jan 2004, Hamburg, ringvorlesung Protein sequence design - fact fiction and fraud (have a look at the slides).
• Wednesday 17 Dec 2003, Hamburg, ringvorlesung Protein structure prediction - 25 years of defeat and disaster
• Wednesday 10 Dec 2003, Hamburg, ringvorlesung Fake degrees of freedom

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.