LABIC - Bioinformatics and Computational Intelligence Laboratory

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UTFPR-HP3DSC: Protein Structures in 3D-HP-SC

1. Introduction

This dataset is related to the Protein Folding Problem (PFP).  There are several models for representing proteins, from the atom level to coarse-grained models. At the atomic level, computational simulations are often unfeasible. Therefore, simplified models (coarse-grained) are used and, amongst them, the HP model is the most frequently used in the literature. This model represents a protein as a chain of amino acids which, in turn, are classified simply as Hydrophobic or Polar (Hydrophilic).  There are many variants of the HP model and this work uses a tri-dimensional version (3D) that represents the hydrophobicity of amino acids as a side chain (SC). There are few works in the literature that explore the 3D-HP-SC. 

2. Description of the dataset:

3. Link to the dataset:  

4. Related Papers:

• Nunes, L.F., Galvão, L.C., Lopes, H.S., Moscato, P., Berretta, R., An integer programming model for protein structure prediction using the 3D-HP side chain model. Discrete Applied Mathematics, v. 198, p. 2-6-214, 2015
• Galvão, L.C., Nunes, L.F., Lopes, H.S., Moscato, P., A new greedy heuristic for 3DHP protein struture prediction with side chain. In: IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW), 2012, Philadelphia, p. 77-10, 2012.
• Benítez, C.V., Scalabrin, M.H., Lopes, H. S., Erig Lima, C.R., Reconfigurable hardware computing for accelerating protein folding simulations using the harmony search algorithm and the 3D-HP-side chain model. In: Proc. 1st IEEE International Workshop on Parallel Architectures for Bioinformatics Systems, 2011, Melbourne, Austrália. Proceedings of the IEEE HARDBIO, Lecture Notes in Computer Science, v. 7017, p. 363-374, 2011.
• Benítez, C.M., Lopes, H.S. Protein structure prediction with the 3D-HP side-chain model using a master-slave parallel genetic algorithm. Journal of the Brazilian Computer Society, v. 16, n. 1, p. 69-78, 2010.
• Benítez, C.M.V, Lopes, H.S., Parallel artificial bee colony algorithm approaches for protein structure prediction using the 3DHP-SC model. In: Essaaidi M., Malgeri M., Badica C. (eds) Intelligent Distributed Computing IV. Studies in Computational Intelligence, vol 315. Springer, Berlin, Heidelberg, 2010.
• Benítez, C.M.V, Lopes, H.S., Protein folding with 3DHP Side-chain model using a hierarchical parallel genetic algorithm. Proc. of IEEE Systems, Man and Cybernetics Conference, Istambul, Turkey, p. 2669 - 2676, 2010.