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Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations
Guo, Yuzhen1; Tao, Fengying1; Wu, Zikai4,5; Wang, Yong2,3
AbstractBackground: Predicting protein structure from amino acid sequence is a prominent problem in computational biology. The long range interactions (or non-local interactions) are known as the main source of complexity for protein folding and dynamics and play the dominant role in the compact architecture. Some simple but exact model, such as HP model, captures the pain point for this difficult problem and has important implications to understand the mapping between protein sequence and structure. Results: In this paper, we formulate the biological problem into optimization model to study the hydrophobic-hydrophilic model on 3D square lattice. This is a combinatorial optimization problem and known as NP-hard. Particle swarm optimization is utilized as the heuristic framework to solve the hard problem. To avoid premature in computation, we incorporated the Tabu search strategy. In addition, a pulling strategy was designed to accelerate the convergence of algorithm based on the characteristic of native protein structure. Together a novel hybrid method combining particle swarm optimization, Tabu strategy, and pulling strategy can fold the amino acid sequences on 3D square lattice efficiently. Promising results are reported in several examples by comparing with existing methods. This allows us to use this tool to study the protein stability upon amino acid mutation on 3D lattice. In particular, we evaluate the effect of single amino acid mutation and double amino acids mutation via 3D HP lattice model and some useful insights are derived. Conclusion: We propose a novel hybrid method to combine several heuristic strategies to study HP model on 3D lattice. The results indicate that our hybrid method can predict protein structure more accurately and efficiently. Furthermore, it serves as a useful tools to probe the protein stability on 3D lattice and provides some biological insights.
KeywordProtein structure prediction HP model 3D lattice Particle swarm optimization Protein stability
Funding ProjectChinese Academy of Sciences[XDB13000000] ; National Natural Fund[11601288] ; National Natural Fund[11422108] ; National Natural Fund[61621003] ; National Natural Fund[61304178]
WOS Research AreaMathematical & Computational Biology
WOS SubjectMathematical & Computational Biology
WOS IDWOS:000411365600010
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Document Type期刊论文
Corresponding AuthorGuo, Yuzhen
Affiliation1.Nanjing Univ Aeronaut & Astronaut, Dept Math, Nanjing 210000, Jiangsu, Peoples R China
2.Chinese Acad Sci, Acad Math & Syst Sci, Natl Ctr Math & Interdisciplinary Sci, Beijing 100190, Peoples R China
3.Univ Chinese Acad Sci, Beijing 100049, Peoples R China
4.Univ Shanghai Sci & Technol, Shanghai 200433, Peoples R China
5.Fudan Univ, Shanghai Key Lab Intelligent Informat Proc, Shanghai 200433, Peoples R China
Recommended Citation
GB/T 7714
Guo, Yuzhen,Tao, Fengying,Wu, Zikai,et al. Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations[J]. BMC SYSTEMS BIOLOGY,2017,11:13.
APA Guo, Yuzhen,Tao, Fengying,Wu, Zikai,&Wang, Yong.(2017).Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations.BMC SYSTEMS BIOLOGY,11,13.
MLA Guo, Yuzhen,et al."Hybrid method to solve HP model on 3D lattice and to probe protein stability upon amino acid mutations".BMC SYSTEMS BIOLOGY 11(2017):13.
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