基于CLP的蛋白质片段组装
CLP-based protein fragment assembly
摘要：
本文研究了一种基于约束逻辑程序设计（CLP）的新方法，通过片段组装来预测蛋白质的三维构象。这些片段是由一个预处理器从已知蛋白质结构的数据库中提取的，该数据库也是为这项工作开发的，它根据相似性和频率对片段进行聚类和分类。将片段组装成完整构象的问题映射为约束求解问题，并使用CLP求解。基于约束的模型使用中等离散度的Ca-侧链质心蛋白质模型，该模型提供了空间填充的效率和良好的近似。该方法适用于现有的能量模型的蛋白质表示，并适用于一个大的邻居搜索策略。结果表明了该方法的可行性和有效性。解决方案的声明性质允许包括未来的扩展，例如，不同大小的碎片以获得更好的准确性。
英文摘要：
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a database of known protein structures that clusters and classifies the fragments according to similarity and frequency. The problem of assembling fragments into a complete conformation is mapped to a constraint solving problem and solved using CLP. The constraint-based model uses a medium discretization degree Ca-side chain centroid protein model that offers efficiency and a good approximation for space filling. The approach adapts existing energy models to the protein representation used and applies a large neighboring search strategy. The results shows the feasibility and efficiency of the method. The declarative nature of the solution allows to include future extensions, e.g., different size fragments for better accuracy.
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