Predicting the 3D structure of difficult proteins

Report
List of participants
Photos

Report ... (draft)

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 the prediction of difficult proteins and membrane proteins, as highlighted by the lists of lectures in the enclosed program.

The main topics were...

• An introduction to structural genomics and the ESF program
  (Mike Taussig)
• The state of art of membrane protein crystallisation
  (Hartmut Michel)
• The protein folding problem
  (Arthur Lesk)
• The constraints that membranes pose on the structure of membrane proteins
  (Stephen White)
• The role played by Bioinformatics on predicting the structural characteristics of G protein coupled receptor
  (Gert Vriend)
• The problems of reliable annotation for membrane proteins in SwissProt
  (Steffen Moeller)
• How to link structures to functions
  (Alfonso Valencia)
• The achievements and limits of comparative modelling
  (Marc Marti' Renom and Anna Tramontano)
• The problem of predicting long loops and how to overcome them
  (Amiram Goldblum)
• Fold recognition methods for a better annotation of genomic sequences
  (David Jones and Michael Sternberg)
• The state of art of ab initio protein structure prediction and the results of the last CASP4 meeting
  (Arthur Lesk)
• The relevance of machine learning methods in protein structure predictions
  (Pierre Baldi)
• The role of protein contacts in determining the correct protein folds
  (Michele Vendruscolo)
• The prediction of stability and topology of all alpha proteins of the inner membrane
  (Gunnar von Heijne, Anders Krogh and Stephen White)
• The prediction of the topology of beta barrel membrane proteins
  (Rita Casadio)

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. 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 gave the opportunity to some of the students to present to all the participants their work in the field of structural genomics. Other students, prompted by the lectures they had had, organised their presentation at once with the chairpersons. This can be considered a good indication of the participation of the students to the school.

List of participants ...

Some candid snaps from the meeting ...