News from CP 2012

Dear readers,

This is a short post from the 18-th International Conference on Principles and Practice of Constraint Programming.

Alessandro Dal Palu’ presenting the impact on the use of constraints in protein flexibility analysis.

We presented our paper: “A Filtering Technique for Fragment Assembly-based Proteins Loop Modeling with Constraints”. The talk focused on the use of novel constraints and propagation to speed up the analysis of flexible regions of proteins.
Protein flexibility is of fundamental importance to understand the ways in which drugs exert biological effects. In particular the study of their binding-site location, biding orientation and binding kinetics is of interest to study how the affinity between a drug and its target could be increased.
In the work presented at CP’12 we focused on testing the capabilities of FIASCO in producing biologically meaningful and efficient results for the problem of protein loop sampling. A link to the slides presented at CP’12 can be found here.

Ferdinando Fioretto (left) and Alessandro Dal Palu’ (right) at the poster session of CP’12.

The positive results produced by FIASCO and the good feedback obtained from the Constraints community is a great signal that Constraint Programming Technologies are a successful solution to tackle problems related to protein flexibility structure analysis.

We are currently working on a new version of FIASCO, which will be able to generate protein structures ensemble uniformly distributed over a specific region of the euclidean space. This is useful for example in drug design, where a number of energetically similar protein conformations is assumed to pre-exist and the interaction between the ligand (drug) and the protein is simulated employing such structure ensemble.

It’s now time to go back to work!

Ferdinando.

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