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Currently viewing: 14 - 17 October | 2008 | Barcelona Supercomputing Center | Spain

About the Course

The prediction and analysis in silico of protein-protein interaction plays an increasing role in functional genomics. The course will present  methods based on docking that predict how two proteins interact when  their three-dimensional structure is known.

Update: ** Final Programme available HERE

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Classes will cover the major  algorithms for rigid-body docking, methods to predict and simulate  conformation changes, scoring functions and refinement procedures, the  use of non-structural information in docking, the assessment of the  methods on benchmarks and in blind predictions. Half of the course will  be practicals in which actual calculations will be performed on  biological problems of interest to the students.


We aim to have a mix of Ph.D. students and junior research fellows in  bioinformatics, and of molecular biologists and structural biologists  who study protein-protein interaction by experiment.

To all participants we will convey the same message: the in silico analysis of protein-protein  interaction is not a substitute, but a useful complement to biochemical  and structural studies.

We will introduce state-of-the-art procedures for this analysis, and explicit the conditions under which it can be  done efficiently and reliably.



Classes and practicals will be on the same site. Lecturers and students  will be housed together. The pauses between classes and the poster session with drinks will offer the opportunity for discussion. Lecturers will participate in the final summing-up.

The practicals will allow students to do actual large-scale calculations, either locally or on remote computer sites. Students will be encouraged to set up procedures and perform calculations on  biological systems of their own choice, especially on those they do  experimental work on.

They will run several established docking procedures under the supervision of instructors who are experts in these procedures, and have access to at least three Web servers performing  protein-protein docking. We will contact the managers of the servers, whether in Europe or in the US, and arrange that they interact by e-mail with the students.

click image to view/download poster

The last day will be devoted to a detailed analysis of the results of the calculations, a comparison of the procedures' performances, and an evaluation of the predictions against experimental  results.

"There is no registration fee, and for academics, room and board are covered by EMBO"




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