Ab-Initio Protein Folding Using Molecular Dynamics and a Simplified Off-Lattice Model

This paper presents an application of Molecular Dynamics (MD) to the Protein Folding Problem (PFP) using a simplified off-lattice model of proteins (3D-AB). To the best of our knowledge, this paper presents the first application of MD to the PFP using globular protein sequences represented with the 3DAB model. The methodology is explained in details. Five synthetic sequences and four real globular proteins sequences were used for testing the approach. Results show that the method is capable of creating realistic folds of the proteins, displaying biological features such as hydrophobic core formation and protein breathing. Future works will investigate more efficient parallel processing methods and the creation of new benchmarks. Keywords-Molecular Dynamics; protein folding problem; 3D-AB model

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