Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
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DOI：
10.1002/prot.22234
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发表时间：
2009-04-01
影响因子：
2.9
通讯作者：
Labute, Paul
中科院分区：
文献类型：
--
作者：
Labute, Paul
提出了一种称为 Protonate3D 的新方法，用于根据大分子结构重原子的 3D 坐标自动预测氢坐标。 Protonate3D 会考虑所有化学基团、配体和溶剂的侧链“翻转”、旋转异构体、互变异构体和电离状态，前提是参数文件中提供了合适的模板。能量模型包括范德华效应、库仑效应、溶剂化效应、旋转异构体、互变异构体和滴定效应。计算验证实验的结果表明Protonate3D可以准确预测大分子结构中氢原子的位置。
A new method, called Protonate3D, is presented for the automated prediction of hydrogen coordinates given the 3D coordinates of the heavy atoms of a macromolecular structure. Protonate3D considers side-chain "flip," rotamer, tautomer, and ionization states of all chemical groups, ligands, and solvent, provided suitable templates are available in a parameter file. The energy model includes van der Waals, Coulomb, solvation, rotamer, tautomer, and titration effects. The results of computational validation experiments suggest that Protonate3D can accurately predict the location of hydrogen atoms in macromolecular structures.