A Molecular Model for Representing Protein Structures and its Application to Protein Folding

The protein folding problem is a central issue in Bioinformatics. It still represents a challenge for both Biology and Computer Science. Proteins are composed by up to hundreds of amino acids, each one with tenths of atoms. In general, a full representation of such structure and its interacting elements precludes computational simulations. This work proposes a molecular model for representing protein structures. This new model preserves some physico-chemical properties of the original protein and is aimed at allowing efficient computational simulations. A simulation of the model using a multiagents system is reported. Results so far suggest the adequacy of the proposed model for representing protein structures and their folding process with a reasonable complexity and suitable expressiveness.