ModFlex: Towards Function Focused Protein Modeling.
ModFlex: Towards Function Focused Protein Modeling.
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DOI：
10.1016/j.jmb.2021.166828
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发表时间：
2021-05-28
影响因子：
5.6
通讯作者：
Godzik A
中科院分区：
文献类型：
--
作者：
Sedova M;Jaroszewski L;Iyer M;Li Z;Godzik A
仅通过氨基酸序列已知的蛋白质数量与通过直接实验确定的结构特征之间存在着广泛且不断扩大的差距。为了缩小这一差距，我们主要依靠基于同源性的推理和建模，通过使用同源蛋白质的结构作为模板来推理未表征蛋白质的结构。随着蛋白质数据库规模的快速增长，通常有多种模板选择，包括来自同一蛋白质的多组坐标。在相同蛋白质的不同实验结构之间观察到的实质性构象差异通常反映了功能相关的结构灵活性。因此，根据所问的问题，使用远距离同源物，或具有较低分辨率但以适当的函数形式求解的坐标集，作为模板可能更具信息性。ModFlex服务器（https：//modflex.org/）通过为用户提供具有多个选项和工具的界面来选择最相关的模板并探索可用模板中的结构多样性范围，从而解决了标准同源性建模方法中很少提及的这一差距。ModFlex与我们团队开发的一系列其他程序和服务器紧密集成，用于分析和可视化蛋白质结构的灵活性和差异。
There is a wide, and continuously widening, gap between the number of proteins known only by their amino acid sequence versus those structurally characterized by direct experiment. To close this gap, we mostly rely on homology-based inference and modeling to reason about the structures of the uncharacterized proteins by using structures of homologous proteins as templates. With the rapidly growing size of the Protein Data Bank, there are often multiple choices of templates, including multiple sets of coordinates from the same protein. The substantial conformational differences observed between different experimental structures of the same protein often reflect function related structural flexibility. Thus, depending on the questions being asked, using distant homologs, or coordinate sets with lower resolution but solved in the appropriate functional form, as templates may be more informative. The ModFlex server (https://modflex.org/) addresses this seldom mentioned gap in the standard homology modeling approach by providing the user with an interface with multiple options and tools to select the most relevant template and explore the range of structural diversity in the available templates. ModFlex is closely integrated with a range of other programs and servers developed in our group for the analysis and visualization of protein structural flexibility and divergence.
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影响因子：
56.9
作者：
Boehr, David D.;McElheny, Dan;Wright, Peter E.
通讯作者：
Wright, Peter E.
影响因子：
64.8
作者：
Eisenmesser, EZ;Millet, O;Kern, D
通讯作者：
Kern, D
影响因子：
56.9
作者：
FRAUENFELDER, H;SLIGAR, SG;WOLYNES, PG
通讯作者：
WOLYNES, PG
DOI：
10.1093/database/baw038
发表时间：
2016-03-28
影响因子：
5.8
作者：
Miguel Monzon, Alexander;Oscar Rohr, Cristian;Parisi, Gustavo
通讯作者：
Parisi, Gustavo
DOI：
10.1093/bioinformatics/btq662
发表时间：
2011-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Benkert P;Biasini M;Schwede T
通讯作者：
Schwede T