Computational Modeling and Simulation Section, National Institute for Interdisciplinary Science and Technology (CSIR), Trivandrum, India.
J Mol Model. 2011 Feb;17(2):401-13. doi: 10.1007/s00894-010-0736-2. Epub 2010 May 19.
A hydrogen bond prediction tool HBPredicT is developed for detecting structural water molecules and CH···π interactions in PDB files of protein-ligand complexes. The program adds the missing hydrogen atoms to the protein, ligands, and oxygen atoms of water molecules and subsequently all the hydrogen bonds in the complex are located using specific geometrical criteria. Hydrogen bonds are classified into various types based on (i) donor and acceptor atoms, and interactions such as (ii) protein-protein, (iii) protein-ligand, (iv) protein-water, (v) ligand-water, (vi) water-water, and (vii) protein-water-ligand. Using the information in category (vii), the water molecules which form hydrogen bonds with the ligand and the protein simultaneously-the structural water-is identified and retrieved along with the associated ligand and protein residues. For CH···π interactions, the relevant portions of the corresponding structures are also extracted in the output. The application potential of this program is tested using 19 HIV-1 protease and 11 PTP1B inhibitor complexes. All the systems showed presence of structural water molecules and in several cases, the CH···π interaction between ligand and protein are detected. A rare occurrence of CH···π interactions emanating from both faces of a phenyl ring of the inhibitor is identified in HIV-1 protease 1D4L.
开发了一种氢键预测工具 HBPredicT，用于检测蛋白质-配体复合物的 PDB 文件中的结构水分子和 CH···π 相互作用。该程序会向蛋白质、配体和水分子的氧原子添加缺失的氢原子，然后使用特定的几何标准来定位复合物中的所有氢键。氢键根据（i）供体和受体原子以及（ii）蛋白质-蛋白质、（iii）蛋白质-配体、（iv）蛋白质-水、（v）配体-水、（vi）水-水和（vii）蛋白质-水-配体等相互作用进行分类。使用类别 (vii) 中的信息，可以识别同时与配体和蛋白质形成氢键的水分子——结构水，并与相关的配体和蛋白质残基一起检索。对于 CH···π 相互作用，也会在输出中提取相应结构的相关部分。使用 19 个 HIV-1 蛋白酶和 11 个 PTP1B 抑制剂复合物测试了该程序的应用潜力。所有系统都显示存在结构水分子，在某些情况下，还检测到配体和蛋白质之间的 CH···π 相互作用。在 HIV-1 蛋白酶 1D4L 中，鉴定出抑制剂苯环两侧均存在 CH···π 相互作用的罕见情况。
