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2017-03-16 发布于天津
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Protein contact maps A binary depiction of protein 3D structures.pdf

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Protein contact maps A binary depiction of protein 3D structures.pdf

Physica A 465 (2017) 782–791 Contents lists available at ScienceDirect Physica A journal homepage: /locate/physa Minireview Protein contact maps: A binary depiction of protein 3D structures Isaac Arnold Emerson ?, Arumugam Amala Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore-632014, Tamil Nadu, India article info Article history: Received 4 January 2016 Received in revised form 25 June 2016 Available online 29 August 2016 Keywords: Protein structure prediction Contact map Complex network abstract In recent years, there has been a considerable interest in examining the structure and dynamics of complex networks. Proteins in 3D space may also be considered as complex systems emerged through the interactions of their constituent amino acids. This representation provides a powerful framework to uncover the general organized principle of protein contact network. Here we reviewed protein contact map in terms of protein structure prediction and analyses. In addition, we had also discussed the various computational techniques for the prediction of protein contact maps and the tools to visualize contact maps. ? 2016 Elsevier B.V. All rights reserved. Contents 1. Introduction 782 2. Construction of protein contact map 783 3. Protein structures as complex networks 783 4. Common methods in protein 3D structure prediction 785 5. Protein 3D structure prediction from contact maps 786 6. Protein contact map prediction 786 6.1. Sequence similarity and multiple sequence alignment methods 787 6.2. Machine learning approaches 788 7. Summary of protein contact maps 789 8. Conclusion 789 Acknowledgements 790 References 790 1. Introduction Proteins are the most abundant organic molecules in living systems. These molecules are much more diverse in structure and function than other classes of macromolecules. At any given point of time, the living system contains thousands of proteins within a single cell and each with a unique function. Pro