Hot Topics in Structural Genomics

Report

The training course organised in Bologna and partially supported by ESF had provided a unique forum for experts and students, mostly young researchers, to meet and fruitfully debate recent and successful achievements in the field of protein structure prediction. The focus has been specifically on hot topics in structural genomics, including recent CASP results, recent and promising large scale genome prediction, protein-protein interactions, protein-DNA interactions and genome functional annotation.

Main topics have been:
· Contemporary challenges in structure prediction and the CASP5 experiment (John Moult)
· Contemporary challenges in structure prediction (Anna Tramontano)
· Prediction of protein structure and function on genomic scale (Jeffrey Skolnick)
· Advanced automated machine learning approaches (David Jones)
· Fully automated ab initio protein structure prediction (Chris Bystroff)
· Automatic fold recognition prediction (Daniel Fischer)
· Prediction of protein function (Arthur Lesk)
· Microarray data analysis and mining (Raffaele Calogero)
· Membrane proteins and their prediction (Gunnar von Heijne, Stephen White)
· Application of tools of structural genomics for genome annotation (Rita Casadio)
· Prediction of protein function (Soeren Brunak, Alffonso Valencia)
· The CAPRI experiment and the prediction of protein-protein interactions (Joel Janin)
· Prediction of protein complexes based on evolution information (Patrick Aloy)
· Prediction of protein-DNA complexes (Sue Jones)
· Prediction of functional patches in proteins (Manuela Helmer Citterich, Nir Ben Tal)

At the completion of the course, participants had been exposed to the presently most debated subjects of protein structure prediction including the basic problems related to wide scale prediction of entire genomes, the problem of protein annotation and the most recent results out of two international experiments: CASP5 and CAPRI, for predicting protein structures and protein-protein interaction, respectively. Furthermore lectures had been generally given in such a way to give first an introduction to the subject and then a more specific overview depending on the speaker's research field. In this way, also those students who were new to the field could grasp some basic principles before entering the details eventually related to the handling of some specific methods. All the lecturers gave enough information and provided examples to elucidate their own work in a comprehensive and explicative way. We opened a web site where speakers were asked to kindly deposit their presentation so that the students could trace back information, useful schemes and web addresses (www.biocomp.unibo.it/school/html2002).

The atmosphere was quite friendly and this promoted discussions between teachers and students. We also organised an open round table discussion (chaired by Anna Tramontano and Arthur Lesk) that focused on the relevance of Bioinformatics in different experimental fields, including membrane protein characterization (Alessandro Desideri and Richard Wagner, protein structure determination (Henriette Molinari) and protein folding (Bruno Samori'). Student had the opportunity to present posters (the 11 selected abstracts are enclosed) and to discuss their posters among themselves and with the lecturers during lunch time and coffee breaks. By this, discussion was therefore promoted and encouraged in a very friendly and open way.

List of speakers

List of Participants