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Modeling conformational transitions in kinases by molecular dynamics simulations: achievements difficulties and open challenges

机译：通过分子动力学模拟对激酶的构象转变进行建模：成就困难和挑战

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摘要

Protein kinases work because their flexibility allows to continuously switch from inactive to active form. Despite the large number of structures experimentally determined in such states, the mechanism of their conformational transitions as well as the transition pathways are not easily to capture. In this regard, computational methods can help to shed light on such an issue. However, due to the intrinsic sampling limitations, much efforts have been done to model in a realistic way the conformational changes occurring in protein kinases. In this review we will address the principal biological achievements and structural aspects in studying kinases conformational transitions and will focus on the main challenges related to computational approaches such as molecular modeling and MD simulations.

机译：蛋白质激酶之所以起作用，是因为它们的灵活性可以连续地从无活性形式转变为有活性形式。尽管在这种状态下通过实验确定了大量结构，但它们的构象转变机理以及转变途径并不容易捕获。在这方面，计算方法可以帮助阐明这一问题。然而，由于固有的采样限制，已经进行了许多努力以现实的方式对蛋白质激酶中发生的构象变化进行建模。在这篇综述中，我们将探讨研究激酶构象转变的主要生物学成就和结构方面，并将重点关注与诸如分子建模和MD模拟等计算方法有关的主要挑战。

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期刊名称 Frontiers in Genetics
作者
Marco DAbramo; Neva Besker; Giovanni Chillemi; Alessandro Grottesi;
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作者单位

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年(卷),期 2014(5),-1
年度 2014
页码 128
总页数 5
原文格式 PDF
正文语种
中图分类遗传学;
关键词
molecular dynamics conformational transitions kinases computational modeling conformational pathways;

机译：分子动力学;构象转变;激酶;计算模型;构象途径;

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专利

1. Conformational Transition Pathways of Epidermal Growth Factor Receptor Kinase Domain from Multiple Molecular Dynamics Simulations and Bayesian Clustering [J] . Yan Li, Xiang Li, Weiya Ma Journal of chemical theory and computation: JCTC . 2014,第8期

机译：从多个分子动力学模拟和贝叶斯聚类的表皮生长因子受体激酶结构域的构象过渡途径
2. Exploring the structural basis of conformational heterogeneity and autoinhibition of human cGMP-specific protein kinase Iα through computational modelling and molecular dynamics simulations [J] . Arooma Maryam, Rana Rehan Khalid, Sundeep Chaitanya Vedithi, Computational and Structural Biotechnology Journal . 2020,第1期

机译：通过计算建模和分子动力学模拟探索构象异质性和自动抑制人CGMP特异性蛋白激酶Iα的结构基础
3. Predicting the Conformational Variability of Abl Tyrosine Kinase using Molecular Dynamics Simulations and Markov State Models [J] . Meng Yilin, Gao Cen, Clawson David K., Journal of chemical theory and computation: JCTC . 2018,第5期

机译：采用分子动力学模拟和马尔可夫状态模型预测ABL酪氨酸激酶的构象变化
4. Molecular dynamics simulation of adhesion performance and conformation transition of SAM-modified Cu/Epoxy interface under electric field [C] . Kwok Stephen C.T., Yuen Matthew M.F. International Conference on Thermal, Mechanical and Multi-Physics Simulation and Experiments in Microelectronics and Microsystems . 2014

机译：电场作用下SAM修饰的Cu /环氧界面黏附性能和构象转变的分子动力学模拟
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. Exploring the structural basis of conformational heterogeneity and autoinhibition of human cGMP-specific protein kinase Iα through computational modelling and molecular dynamics simulations [O] . Arooma Maryam, Rana Rehan Khalid, Sundeep Chaitanya Vedithi, 2020

机译：通过计算建模和分子动力学模拟探索构象异质性和自动抑制人CGMP特异性蛋白激酶Iα的结构基础
7. Modeling conformational transitions in kinases by molecular dynamics simulations: achievements, difficulties, and open challenges [O] . D'Abramo, Marco, Besker, Neva, Chillemi, Giovanni, 2014

机译：通过分子动力学模拟对激酶的构象转变进行建模：成就，困难和挑战
8. Molecular Dynamics Simulation of a Model for (One-Dimensional) Structural Phase Transitions. [R] . koehler, t. r. bishop, a. r. 2001

机译：（一维）结构相变模型的分子动力学模拟。

Modeling conformational transitions in kinases by molecular dynamics simulations: achievements difficulties and open challenges

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