Wojciechowski Marek
Department of Pharmaceutical Technology and Biochemistry, Gdansk University of Technology, ul. Narutowicza 11/12, 80-233 Gdańsk, Poland.
J Mol Graph Model. 2017 Nov;78:74-80. doi: 10.1016/j.jmgm.2017.09.016. Epub 2017 Sep 23.
A set of high quality structures of protein-ligand complexes with experimentally determined binding affinities has been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on the new dataset much better correlation between the computed and experimentally determined binding affinities was achieved and the quality of pose prediction improved even more.
从蛋白质数据库中提取了一组具有实验测定结合亲和力的高质量蛋白质-配体复合物结构，并用于测试和重新校准AutoDock力场。由于对于某些结合位点，水分子对于桥接受体-配体相互作用至关重要，因此必须将它们纳入分析。为了简化将水分子纳入结合位点的过程并使其不那么模糊，创建了新的简单水模型。在新数据集上重新校准力场后，计算得到的和实验测定的结合亲和力之间实现了更好的相关性，并且构象预测的质量提高得更多。
