基于疏水核心预测残基间接触簇
Prediction of inter-residue contact clusters from hydrophobic cores.
作者信息
Chen Peng, Liu Chunmei, Burge Legand, Mahmood Mohammad, Southerland William, Gloster Clay
机构信息
Department of Systems and Computer Science, Howard University, 2400 Sixth Street, NW Washington, DC 20059, USA.
出版信息
Int J Data Min Bioinform. 2008 Dec 11;2008:703-708. doi: 10.1109/ICMLA.2008.74.
A contact map is a key factor representing a specific protein structure. To simplify the protein contact map prediction, we predict the inter-residue contact clusters centered at the groups of their surrounding inter-residue contacts. In this paper, we adopt a Support Vector Machine (SVM)-based approach to predict the inter-residue contact cluster centers. The input of the SVM predictor includes sequence profile, evolutionary rate and predicted secondary structure. The SVM predictor is based on hydrophobic cores that may be considered as locations of the inter-residue contact clusters. About 35% of clustering centers of inter-residue contacts can be predicted accurately.
接触图是表示特定蛋白质结构的关键因素。为了简化蛋白质接触图预测，我们预测以其周围残基间接触基团为中心的残基间接触簇。在本文中，我们采用基于支持向量机（SVM）的方法来预测残基间接触簇中心。SVM预测器的输入包括序列概况、进化速率和预测的二级结构。SVM预测器基于疏水核心，疏水核心可被视为残基间接触簇的位置。约35%的残基间接触聚类中心能够被准确预测。
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