Scatter Search for Homology Modeling

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• 关键词：Comparative modeling ; Homology modeling ; Protein structure prediction ; Scatter search ; Metaheuristics
• 刊名：Lecture Notes in Computer Science
• 出版年：2016
• 出版时间：2016
• 年：2016
• 卷：9712
• 期：1
• 页码：66-73
• 全文大小：491 KB
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• 作者单位：Mouses Stamboulian (16)
  Nashat Mansour (16)
  
  16. Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
  
• 丛书名：Advances in Swarm Intelligence
• ISBN：978-3-319-41000-5
• 刊物类别：Computer Science
• 刊物主题：Artificial Intelligence and Robotics
  Computer Communication Networks
  Software Engineering
  Data Encryption
  Database Management
  Computation by Abstract Devices
  Algorithm Analysis and Problem Complexity
  
• 出版者：Springer Berlin / Heidelberg
• ISSN：1611-3349
• 卷排序：9712

文摘

Homology modeling is an effective technique in protein structure prediction (PSP). However this technique suffers from poor initial target-template alignments. To improve homology based PSP, we propose a scatter search (SS) metaheuristic algorithm. SS is an evolutionary approach that is based on a population of candidate solutions. These candidates undergo evolutionary operations that combine search intensification and diversification over a number of iterations. The metaheuristic optimizes the initial poor alignments and uses fitness functions. We assess our algorithm on a number of proteins whose structures are present in the Protein Data Bank and which have been used in previous literature. Results obtained by our SS algorithm are compared with other approaches. The 3D models predicted by our algorithm show improved root mean standard deviations with respect to the native structures.