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. 2014 Feb 10;4(1):160–180. doi: 10.3390/biom4010160

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© 2014 by the authors; licensee MDPI, Basel, Switzerland.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).

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A pentapeptide structure is processed by the Neural Network Pairwise Interaction Fields (NNPIF). The structure is represented as a directed acyclic graph (DAG) by considering as leaf nodes the interactions between couples of atoms. Each interaction is modeled by the function, F(), via an NN, N^F. The inputs encode characteristics of each of the two interacting atoms (a_x, a_y) in the pair and their interaction (d_xy). The outputs are combined in hidden vectors Y. The contribution of each interaction to the quality of the structure is modeled by the function, G(), via an NN, N^G, which produces the global output, O.