MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
MOLE 2.0: advanced approach for analysis of biomacromolecular channels.
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DOI：
10.1186/1758-2946-5-39
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发表时间：
2013-08-16
影响因子：
8.6
通讯作者：
Koča J
中科院分区：
文献类型：
--
作者：
Sehnal D;Svobodová Vařeková R;Berka K;Pravda L;Navrátilová V;Banáš P;Ionescu CM;Otyepka M;Koča J
生物大分子（蛋白质、核酸及其复合物）中的通道和孔发挥着重要的生物学作用，例如，分子识别和酶底物特异性。我们提出了一个先进的软件工具，名为MOLE 2.0，它已被设计用于分析分子通道和孔。对其他可用软件工具的基准测试表明，MOLE 2.0相比之下更快，更强大，更通用。作为一项新功能，MOLE 2.0估计所识别通道的物理化学性质，即，亲水性、疏水性、极性、电荷和可变性。我们还评估了细胞色素P450超家族的两个成员的80个X射线结构的物理化学性质的变化。在选定的生物大分子中识别的通道的估计的物理化学性质对应以及与各自的通道的已知功能。因此，预测的物理化学性质可以提供关于所识别的通道的潜在功能的有用信息。MOLE 2.0软件可在http://mole.chemi.muni.cz上获得。
Channels and pores in biomacromolecules (proteins, nucleic acids and their complexes) play significant biological roles, e.g., in molecular recognition and enzyme substrate specificity. We present an advanced software tool entitled MOLE 2.0, which has been designed to analyze molecular channels and pores. Benchmark tests against other available software tools showed that MOLE 2.0 is by comparison quicker, more robust and more versatile. As a new feature, MOLE 2.0 estimates physicochemical properties of the identified channels, i.e., hydropathy, hydrophobicity, polarity, charge, and mutability. We also assessed the variability in physicochemical properties of eighty X-ray structures of two members of the cytochrome P450 superfamily. Estimated physicochemical properties of the identified channels in the selected biomacromolecules corresponded well with the known functions of the respective channels. Thus, the predicted physicochemical properties may provide useful information about the potential functions of identified channels. The MOLE 2.0 software is available at http://mole.chemi.muni.cz.
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DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
56.9
作者：
Doyle, DA;Cabral, JM;MacKinnon, R
通讯作者：
MacKinnon, R
影响因子：
5.6
作者：
L端demann, SK;Lounnas, V;Wade, RC
通讯作者：
Wade, RC
影响因子：
--
作者：
Huang B;Schroeder M
通讯作者：
Schroeder M
影响因子：
4.8
作者：
Biedermannova, Lada;Prokop, Zbynek;Wade, Rebecca C.
通讯作者：
Wade, Rebecca C.