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

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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 3D-AB 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.
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Document Type: Research Article

Publication date: August 1, 2013

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  • Bionanoscience attempts to harness various functions of biological macromolecules and integrate them with engineering for technological applications. It is based on a bottom-up approach and encompasses structural biology, biomacromolecular engineering, material science, and engineering, extending the horizon of material science. The journal aims at publication of (i) Letters (ii) Reviews (3) Concepts (4) Rapid communications (5) Research papers (6) Book reviews (7) Conference announcements in the interface between chemistry, physics, biology, material science, and technology. The use of biological macromolecules as sensors, biomaterials, information storage devices, biomolecular arrays, molecular machines is significantly increasing. The traditional disciplines of chemistry, physics, and biology are overlapping and coalescing with nanoscale science and technology. Currently research in this area is scattered in different journals and this journal seeks to bring them under a single umbrella to ensure highest quality peer-reviewed research for rapid dissemination in areas that are in the forefront of science and technology which is witnessing phenomenal and accelerated growth.
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