SDM: a server for predicting effects of mutations on protein stability.
SDM: a server for predicting effects of mutations on protein stability.
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DOI：
10.1093/nar/gkx439
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发表时间：
2017-07-03
影响因子：
14.9
通讯作者：
Blundell TL
中科院分区：
文献类型：
--
作者：
Pandurangan AP;Ochoa-Montaño B;Ascher DB;Blundell TL
在这里，我们报告了一个用于改进SDM的网络服务器，用于预测突变对蛋白质稳定性的影响。作为一种开创性的基于知识的方法，SDM被强调为与许多其他方法结合使用的最合适的方法。我们基于目前扩展的PDB(信息量增加了5倍)更新了特定于环境的氨基酸替换表，并引入了新的残基构象和相互作用参数，包括堆积密度和残基深度。更新的服务器已经使用包含来自132个不同蛋白质结构的2690个点突变的基准进行了广泛的测试。修订后的方法与假设的反向突变具有很好的相关性，比使用机器学习方法建立的可比方法更好，突显了我们基于知识的方法在识别稳定突变方面的优势。给定PDB文件(包含蛋白质原子的3D坐标的蛋白质数据库文件格式)和点突变，服务器计算野生型和突变型蛋白质之间的稳定性差异分数。该服务器可在http://structure.bioc.cam.ac.uk/sdm2上获得
Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid substitution tables based on the current expanded PDB (a 5-fold increase in information), and introduced new residue-conformation and interaction parameters, including packing density and residue depth. The updated server has been extensively tested using a benchmark containing 2690 point mutations from 132 different protein structures. The revised method correlates well against the hypothetical reverse mutations, better than comparable methods built using machine-learning approaches, highlighting the strength of our knowledge-based approach for identifying stabilising mutations. Given a PDB file (a Protein Data Bank file format containing the 3D coordinates of the protein atoms), and a point mutation, the server calculates the stability difference score between the wildtype and mutant protein. The server is available at http://structure.bioc.cam.ac.uk/sdm2
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影响因子：
2.9
作者：
Li, Yunqi;Zhang, Jian;Tai, David;Middaugh, C. Russell;Zhang, Yang;Fang, Jianwen
通讯作者：
Fang, Jianwen
影响因子：
5.6
作者：
Fleming, PJ;Richards, FM
通讯作者：
Richards, FM
影响因子：
5.8
作者：
Huang, Liang-Tsung;Gromiha, M. Michael;Ho, Shinn-Ying
通讯作者：
Ho, Shinn-Ying
影响因子：
8
作者：
Bullock, AN;Henckel, J;Fersht, AR
通讯作者：
Fersht, AR
影响因子：
3.7
作者：
Gong S;Blundell TL
通讯作者：
Blundell TL