Identification of ATP binding residues of a protein from its primary sequence.
Identification of ATP binding residues of a protein from its primary sequence.
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DOI：
10.1186/1471-2105-10-434
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发表时间：
2009-12-19
影响因子：
3
通讯作者：
Raghava GP
中科院分区：
文献类型：
--
作者：
Chauhan JS;Mishra NK;Raghava GP
后基因组时代的主要挑战之一是为基因组测序计划中产生的大量蛋白质提供功能注释。许多蛋白质的功能取决于它们与小分子或配体的相互作用。ATP是一种重要的配体，在许多蛋白质的功能中作为辅酶发挥关键作用。为了了解ATP结合蛋白（ATP binding proteins，ABP）与配体相互作用的机制，需要开发鉴定ATP结合蛋白（ATP binding proteins，ABP）中ATP相互作用残基的方法。我们已经比较了蛋白质的ATP相互作用和非相互作用区域的氨基酸组成，并观察到某些残基优选与ATP相互作用。这项研究描述了几个模型，已开发用于识别ATP相互作用的蛋白质中的残基。所有这些模型都在168个非冗余ABP链上进行了训练和测试。首先，我们已经开发了一个支持向量机（SVM）基于模型使用蛋白质的一级序列，并获得最大MCC 0.33的准确率为66.25%。其次，利用PSI-BLAST生成的位置特异性评分矩阵（PSSM）建立了另一个基于SVM的模型。该模型的性能比仅使用蛋白质一级序列的前一个模型有显著提高（MCC 0.5）。这项研究表明，它是有可能预测的“ATP相互作用的残基”在蛋白质中具有中等精度使用其序列。进化信息对于“ATP相互作用残基”的鉴定是重要的，因为与一级序列相比，它提供了更多的信息。该方法对研究ATP结合蛋白的研究具有一定的参考价值。基于这项研究，已经开发了一个网络服务器，用于预测蛋白质中的“ATP相互作用残基”http://www.imtech.res.in/raghava/atpint/。
One of the major challenges in post-genomic era is to provide functional annotations for large number of proteins arising from genome sequencing projects. The function of many proteins depends on their interaction with small molecules or ligands. ATP is one such important ligand that plays critical role as a coenzyme in the functionality of many proteins. There is a need to develop method for identifying ATP interacting residues in a ATP binding proteins (ABPs), in order to understand mechanism of protein-ligands interaction. We have compared the amino acid composition of ATP interacting and non-interacting regions of proteins and observed that certain residues are preferred for interaction with ATP. This study describes few models that have been developed for identifying ATP interacting residues in a protein. All these models were trained and tested on 168 non-redundant ABPs chains. First we have developed a Support Vector Machine (SVM) based model using primary sequence of proteins and obtained maximum MCC 0.33 with accuracy of 66.25%. Secondly, another SVM based model was developed using position specific scoring matrix (PSSM) generated by PSI-BLAST. The performance of this model was improved significantly (MCC 0.5) from the previous one, where only the primary sequence of the proteins were used. This study demonstrates that it is possible to predict 'ATP interacting residues' in a protein with moderate accuracy using its sequence. The evolutionary information is important for the identification of 'ATP interacting residues', as it provides more information compared to the primary sequence. This method will be useful for researchers studying ATP-binding proteins. Based on this study, a web server has been developed for predicting 'ATP interacting residues' in a protein http://www.imtech.res.in/raghava/atpint/.
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影响因子：
14.8
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin
影响因子：
8
作者：
Kaur, H;Raghava, GPS
通讯作者：
Raghava, GPS
影响因子：
8
作者：
Kaur, H;Raghava, GPS
通讯作者：
Raghava, GPS
DOI：
10.1016/j.bbrc.2007.06.027
发表时间：
2007-08-24
影响因子：
3.1
作者：
Chou, Kuo-Chen;Shen, Hong-Bin
通讯作者：
Shen, Hong-Bin
影响因子：
1.6
作者：
Ding, Hui;Luo, Liaofu;Lin, Hao
通讯作者：
Lin, Hao