Protein Folding Simulation in CCP

 
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Type: Conference or Workshop Item (Poster)
Member Organisation: 109 University of Udine, DIMI

Dal Palu', A. and Dovier, A. and Fogolari, F. (2004) Protein Folding Simulation in CCP. In: 20th International Conference, ICLP 2004, 6-10 Sep 2004, Saint-Malo, France.

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Abstract

A protein can be identified by a finite sequence of aminoacids, each of them chosen from a set of 20 elements. The Protein Folding Problem is the problem of predicting the 3D native conformation of a protein, when the sequence of aminoacids composing it is known. This problem is fundamental for biological and pharmaceutical research. The typical length of these sequences is less than 500 aminoacids. Due to intrinsic computational limits, no general solution is available. In particular, simulation-based techniques that take into account all atoms constituting the aminoacids (and the solvent) and simulate the folding process approximating atom interactions, involve a huge number of independent entities, and for each pair of them there are forces of various nature to be computed. As a consequence, simulation programs of this family run extremely slow. Moreover, these programs are typically written in imperative languages and hard to be parallelized. In this paper we present a higher level simulation approach to the problem using concurrent constraint programming. Each aminoacid in the input sequence is viewed as a process that communicates with the others. The implementation in Mozart is rather natural, the code is intrinsically concurrent and thus easy to be parallelized.

Deposited by Alessandro Dal Palu' on 16 February 2005

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