Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy.
Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy.
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DOI：
10.3389/fbioe.2020.558247
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发表时间：
2020
影响因子：
5.7
通讯作者：
Song Y
中科院分区：
文献类型：
--
作者：
Frenz B;Lewis SM;King I;DiMaio F;Park H;Song Y
预测蛋白质在点突变时稳定性变化的软件是解决许多生物技术和科学问题的宝贵工具。为了促进这类软件的开发，并提供对现有实验数据的方便访问，创建了ProTherm数据库。收集信息的方法和类型的偏差导致了可获得实验数据的突变类型的差异。例如，丙氨酸的突变被严重高估，而涉及带电残基的突变，特别是从一个带电残基到另一个带电残基的突变被低估。作为基准集创建的ProTherm子集没有考虑到这一点，通常不能充分代表某些突变类型。这一期将系统性偏差引入到以前发表的协议中，以准确预测这些类型突变上折叠能量的变化。为了解决此问题，我们生成了一个已更正这些问题的新基准集。然后，我们使用基准测试集来测试Rosetta软件套件中点突变能量学工具的一些改进。
Software to predict the change in protein stability upon point mutation is a valuable tool for a number of biotechnological and scientific problems. To facilitate the development of such software and provide easy access to the available experimental data, the ProTherm database was created. Biases in the methods and types of information collected has led to disparity in the types of mutations for which experimental data is available. For example, mutations to alanine are hugely overrepresented whereas those involving charged residues, especially from one charged residue to another, are underrepresented. ProTherm subsets created as benchmark sets that do not account for this often underrepresent tense certain mutational types. This issue introduces systematic biases into previously published protocols’ ability to accurately predict the change in folding energy on these classes of mutations. To resolve this issue, we have generated a new benchmark set with these problems corrected. We have then used the benchmark set to test a number of improvements to the point mutation energetics tools in the Rosetta software suite.
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影响因子：
7.7
作者：
Wang, Ray Yu-Ruei;Song, Yifan;DiMaio, Frank
通讯作者：
DiMaio, Frank
影响因子：
14.8
作者：
Kumar, Prateek;Henikoff, Steven;Ng, Pauline C.
通讯作者：
Ng, Pauline C.
影响因子：
5.6
作者：
Guerois, R;Nielsen, JE;Serrano, L
通讯作者：
Serrano, L
影响因子：
5.6
作者：
Gilis, D;Rooman, M
通讯作者：
Rooman, M
DOI：
10.1016/0005-2795(75)90109-9
发表时间：
1975-01-01
期刊：
BIOCHIMICA ET BIOPHYSICA ACTA
影响因子：
--
作者：
MATTHEWS, BW
通讯作者：
MATTHEWS, BW