Scientific Report of the 2nd ESF training course on
Molecular Interaction: New Frontiers for Computational Methods

Verona, 13-16 July 2004

Organized by: Anna Tramontano, Henriette Molinari and Alfonso Valencia

Report
List of participants

Report (draft)

This workshop was held in Verona on July 13th - 16th 2004 and was devoted to computational methods for predicting and analyzing protein-protein and protein-small molecule interactions. This was the second time we ran such a training course and, as the first was quite successful, we left the structure of the course unchanged. The course was directed towards people with some experience in computational techniques and/or in the usage of docking programs. We received 88 applications and accepted 25 participants, a number that we consider ideal to ensure the success of the practical part. One of the participants had to cancel at the last minute for personal reasons and therefore the course included 24 participants.

The geographical distribution of the applicants and of the accepted participants is shown in the Table below:

The scheme of the workshop was to devote the afternoon to seminars and the mornings to practical work. Five applicants were selected beforehand on the basis of their expertise to help preparing the practicals.

Programme:

Day 1 - Tuesday 13 Arrivals
14:30 Bus from the train station to the University
14:30 - 15:30 Registration and set up of posters
15:30 - 16:00 Welcome and Introduction to the course
Anna Tramontano: Why interactions?
Alfonso Valencia: The ESF programme in Functional Genomics
16:30 - 17:00 Lecture 1 - Alfonso Valencia
Sequence based tools for the prediction of protein protein interaction
17:00-17:30 Coffee break and poster viewing
17:30-18:30 Lecture 2 - Rita Casadio
Automatic learning tools applied to the problem of predicting protein protein interaction
19:00 Bus to town
20:30 Dinner at Restaurant "Tabia'"

Day 2 - Wednesday 14
9:00 Bus to the University
9:30-11:00 Practicals: Text mining
Alfonso Valencia, with the help of Noam Kaplan, Alejandro Giorgetti, James Watson, Michael Tress and Carsten Friis.
11:00-11:30 Coffee break and poster viewing
11:30-13:00 Practicals: Text mining
Alfonso Valencia, with the help of Noam Kaplan, Alejandro Giorgetti, James Watson, Michael Tress and Carsten Friis.
13:00-14:30 Lunch
14:30-15:30 Lecture 4 - Anna Tramontano
High-throughput methods for the analysis of protein protein interaction
15:30-16:30 Lecture 5 - Joel Janin
Structural basis for protein protein interaction and CAPRI
16:30-18:00 Coffee break and poster viewing
18:00-19:00 Lecture 6 - David Jones
Methods for the prediction of protein protein interaction
19:00 Bus to town
20:00 Dinner at restaurant "Ropeton"

Day 3 - Thursday 15
9:00 Bus to the University
9:30-11:00 Practicals: Protein protein docking
Anna Tramontano with the help of Noam Kaplan, Alejandro Giorgetti, James Watson, Michael Tress and Carsten Friis.
11:00-11:30 Coffee break and poster viewing
11:30-13:00 Practicals: Protein protein docking
Anna Tramontano, with the help of Noam Kaplan, Alejandro Giorgetti, James Watson, Michael Tress and Carsten Friis.
13:00-14:30 Lunch
14:30-15:30 Lecture 7 - Arthur Lesk
Protein interaction networks
15:30-16:30 Lecture 8 - Uwe Koch
Docking methods for small molecules
16:30-18:00 Coffee break and poster viewing
18:00-19:00 Lecture 9 - Paolo Carloni
QM/MM methods for the prediction of protein small molecole interactions
19:00 Bus to town
20:00 Dinner at restaurant "Il Bracere"

Day 4 - Friday 16
9:00 Bus to the University
9:30-11:00 Practicals: GRID and small molecule docking
Uwe Koch, with the help of Noam Kaplan, Alejandro Giorgetti, James Watson, Michael Tress and Carsten Friis.
11:00-11:30 Coffee break and poster viewing
11:30-13:00 Practicals: GRID and small molecule docking
Uwe Koch, with the help of Noam Kaplan, Alejandro Giorgetti, James Watson, Michael Tress and Carsten Friis.
13:00-14:30 Lunch
14:30-15:00 Closing remarks
15:30 Bus to train station

Each participant had a Linux workstation available:

The programs requiring installation license (e.g. GRID) were pre-installed, while for freely downloadable software (SwissPDBviewer, Rasmol, GRAMM etc.), it was decided to let the participant do the installation themselves as to learn how to do it once back in their lab.
The first afternoon and morning was devoted to sequence base methods for the prediction of protein protein interactions, the lectures discussed several methods (co-evolution, comparative genomics, correlated mutation, neural networks and text mining). The practical consisted in learning how to use several protein interaction resources.
The practical included interaction data bases, servers for predicting interactions, text mining resources and related tools.

The second afternoon and morning was devoted to the analysis and prediction of protein protein interaction on the basis of their structure. Topics such as searching rotational and translation space, scoring functions, blind assessment were discussed.
The practical consisted in docking two proteins (a protease and an inhibitor). The students were provided with the unbound structures of the two proteins. The protease active site was illustrated to them, so that they could use this knowledge to asses the likelihood of the solutions. They used the freely available program GRAMM and analyzed the list of solutions using the SwissPDBViewer visualization package. At the end of the exercise, the experimental structure of the complex was made available to the students who could then compare their evaluation against the experimental structure.

The last afternoon and morning were devoted to a discussion of interaction networks, with all the problems connected with the definition of logical and physical interactions and to the protein - small molecule docking problem. The practical used the program GRID to dock Hexadecanesulfonic acid into the Adipocyte lipid-binding (ALBP).

The practical sessions went reasonable smoothly without any serious technical problem and essentially all the participants were able to complete their exercises.

The atmosphere of the course was rather pleasant. Both the students and the instructors were accommodated in two student housing facilities, they would all meet for breakfast and move to the University by bus. Lunch and coffee breaks were served near the poster room to facilitate discussion and interactions. Pictures of every poster are availabale at the course web site (http://cassandra.bio.uniroma1.it/ESF04)

In the evening, the bus would take the students back to town where dinner was arranged in a local restaurant.

At the end of the course, the participants were asked to fill an on-line questionnaire, whose results are enclosed below. By numerically encoding the answers as:

The following picture arises:

I also took the liberty of inserting a few questions about the gender issue in science, as the organizers are particularly interested in the views of female scientists about this issue. To our satisfaction, the female participants did not feel any discrimination and gave some interesting opinions.

All in all, the participants expressed their satisfaction for the course. It was certainly useful to most of them and, by and large, satisfied their expectation.
The presentations and the pages describing the practical exercise are available in the course web site (http://cassandra.bio.uniroma1.it/ESF04).

List of participants*:
* As per students' request, the address as been typed in such a way that it should not be usable by spamming programs.