EMPIRICAL POTENTIALS FOR ION BINDING IN PROTEINS

SERGEI RAHMANOV  IVAN KULAKOVSKIY  LEONID UROSHLEV  VSEVOLOD MAKEEV

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EMPIRICAL POTENTIALS FOR ION BINDING IN PROTEINS

机译：蛋白质中离子结合的经验势

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Empirical potentials for interaction of proteins with intracellular ions are presented. We derive the potentials using a training dataset of the protein 3D structure bank, PDB, based on the statistical analysis of contacts between ions and protein atoms of different types. The potentials are derived using Monte Carlo Reference State, simulating non-interacting structure elements as random 3D points in the structure space. The resulting potentials are detailed, continuous, and cover a wide range of contact distances. The obtained potentials were tested for prediction of ion-binding sites in proteins and are shown to reproduce locations and specificities of ion-binding sites with a high accuracy. A web server is created for predictions of ion-binding sites in proteins.

机译：提出了蛋白质与细胞内离子相互作用的经验潜力。我们基于蛋白质3D结构库PDB的训练数据集，基于对离子和不同类型的蛋白质原子之间的接触进行统计分析，得出了电位。使用蒙特卡洛参考状态，模拟非交互结构元素作为结构空间中的随机3D点来推导电势。产生的电位是详细的，连续的，并且涵盖了广泛的接触距离。测试所获得的电位以预测蛋白质中的离子结合位点，并显示出可以高精度再现离子结合位点的位置和特异性。创建了一个Web服务器，用于预测蛋白质中的离子结合位点。

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《Journal of Bioinformatics and Computational Biology》 |2010年第3期|p.427-435|共9页
作者
SERGEI RAHMANOV IVAN KULAKOVSKIY LEONID UROSHLEV VSEVOLOD MAKEEV;
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作者单位

Research Institute for Genetics and Selection of Industrial Microorganisms, Genetika, 1 Dorozhny proezd, 1, Moscow 117545, Russia;

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia;

Research Institute for Genetics and Selection of Industrial Microorganisms, Genetika, 1 Dorozhny proezd, 1, Moscow 117545, Russia;

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia;

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正文语种 eng
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关键词
Knowledge-based potentials; ion-binding specificity; proteins.;

机译：基于知识的潜力;离子结合特异性蛋白质。;

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机译：配体蛋白晶体复合物的经验自由能计算1。基于知识的配体蛋白相互作用力在预测人类免疫缺陷病毒1蛋白结合亲和力中的应用
2. Empirical potentials for ion binding in proteins [J] . Rahmanov S., Kulakovskiy I., Uroshlev L., Journal of Bioinformatics and Computational Biology . 2010,第3期

机译：蛋白质中离子结合的经验潜力
3. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy [J] . Rahaman O., Estrada T.P., Doren D.J., Journal of chemical information and modeling . 2011,第9期

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4. Prediction of Polyanion Binding Potential in Proteins Using Random Forest [C] . Jianwen Fang, Nazila Salamat-Miller, Yinghua Dong, International Conference on Bioinformatics and Computational Biology . 2007

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机译：基于线性相互作用有效配体尺寸和经验对电位的若干两步评分功能的评价用于预测蛋白质 - 配体结合几何和自由能
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机译：C组链球菌和“金黄色葡萄球菌”中的纤连蛋白结合蛋白。结合域的鉴定和表征。

EMPIRICAL POTENTIALS FOR ION BINDING IN PROTEINS

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