Prediction of Protein Coarse Contact Maps

Alessandro Vullo; Paolo Frasconi

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Prediction of Protein Coarse Contact Maps

机译：蛋白质粗接触图的预测

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Prediction of topological representations of proteins that are geometrically invariants can contribute towards the solution of fundamental open problems in structural genomics like folding. In this paper we focus on coarse grained protein contact maps, a representation that describes the spatial neighborhood relation between secondary structure elements such as helices, beta sheets, and random coils. Our methodology is based on searching the graph space. The search algorithm is guided by an adaptive evaluation function computed by a specialized noncausal recursive connectionist architecture. The neural network is trained using candidate graphs generated during examples of successful searches. Our results demonstrate the viability of the approach for predicting coarse contact maps.

机译：预测几何上不变的蛋白质的拓扑表示可以有助于解决结构基因组学（如折叠）中的基本开放问题。在本文中，我们着眼于粗粒蛋白质接触图，该图描述了二级结构元素（例如螺旋，β折叠和随机线圈）之间的空间邻域关系。我们的方法基于搜索图空间。搜索算法由专门的非因果递归连接主义体系结构计算的自适应评估功能指导。使用在成功搜索示例期间生成的候选图来训练神经网络。我们的结果证明了预测粗接触图的方法的可行性。

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《Journal of Bioinformatics and Computational Biology》 |2003年第2期|共21页
作者
Alessandro Vullo; Paolo Frasconi;
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正文语种 eng
中图分类细胞生物学;
关键词
protein contact maps; machine learning; recursive neural networks;

机译：蛋白质接触图;机器学习;递归神经网络;

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专利

1. Prediction of Protein Coarse Contact Maps [J] . Alessandro Vullo, Paolo Frasconi Journal of Bioinformatics and Computational Biology . 2003,第2期

机译：蛋白质粗接触图的预测
2. Improving prediction of protein secondary structure, backbone angles, solvent accessibility and contact numbers by using predicted contact maps and an ensemble of recurrent and residual convolutional neural networks [J] . Hanson Jack, Paliwal Kuldip, Litfin Thomas, Bioinformatics . 2019,第14期

机译：通过使用预测的联系地图和经常性和残余卷积神经网络的集合来改善蛋白质二级结构，骨干角，溶剂可访问性和接触号的预测
3. Mining of protein contact maps for protein fold prediction [J] . Bhavani Durga, Suvarnavani K., Sinha Somdatta Wiley interdisciplinary reviews. Data mining and knowledge discovery . 2011,第4期

机译：挖掘蛋白质接触图以预测蛋白质折叠
4. A bi-recursive neural network architecture for the prediction of protein coarse contact maps [C] . Vullo, A., Frasconi, . 2002

机译：用于蛋白质粗接触图预测的双递归神经网络架构
5. Protein structure prediction and conformational transitions. I. Improvement of protein secondary structure prediction. II. Pathways of conformational transition originating in phosphorylation: A study of CDK2 using targeted molecular dynamics and coarse grained models [D] . Cheng, Haitao 2009

机译：蛋白质结构预测和构象过渡。 I.改善蛋白质二级结构预测。 II。源于磷酸化的构象过渡的途径：使用靶分子动力学和粗粒模型的CDK2研究
6. A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations [O] . Vincent Frappier, Rafael J. Najmanovich 2014

机译：粗粒弹性网络原子接触模型及其在蛋白质动力学模拟和突变效应预测中的应用
7. A bi-recursive neural network architecture for the prediction of protein coarse contact maps [O] . Alessandro Vullo, Paolo Frasconi 2002

机译：用于蛋白质粗接触图预测的双递归神经网络架构

Prediction of Protein Coarse Contact Maps

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