Boer D R, Kroon J, Cole J C, Smith B, Verdonk M L
Department of Crystal & Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
J Mol Biol. 2001 Sep 7;312(1):275-87. doi: 10.1006/jmbi.2001.4901.
SuperStar is an empirical method for identifying interaction sites in proteins, based entirely on the experimental information about non-bonded interactions, present in the IsoStar database. The interaction information in IsoStar is contained in scatterplots, which show the distribution of a chosen probe around structure fragments. SuperStar breaks a template molecule (e.g. a protein binding site) into structural fragments which correspond to those in the scatterplots. The scatterplots are then superimposed on the corresponding parts of the template and converted into a composite propensity map. The original version of SuperStar was based entirely on scatterplots from the CSD. Here, scatterplots based on protein-ligand interactions are implemented in SuperStar, and validated on a test set of 122 X-ray structures of protein-ligand complexes. In this validation, propensity maps are compared with the experimentally observed positions of ligand atoms of comparable types. Although non-bonded interaction geometries in small molecule structures are similar to those found in protein-ligand complexes, their relative frequencies of occurrence are different. Polar interactions are more common in the first class of structures, while interactions between hydrophobic groups are more common in protein crystals. In general, PDB and CSD-based SuperStar maps appear equally successful in the prediction of protein-ligand interactions. PDB-based maps are more suitable to identify hydrophobic pockets, and inherently take into account the experimental uncertainties of protein atomic positions. If the protonation state of a histidine, aspartate or glutamate protein side-chain is known, specific CSD-based maps for that protonation state are preferred over PDB-based maps which represent an ensemble of protonation states.
SuperStar是一种用于识别蛋白质中相互作用位点的经验方法，它完全基于IsoStar数据库中存在的关于非键相互作用的实验信息。IsoStar中的相互作用信息包含在散点图中，这些散点图显示了所选探针围绕结构片段的分布。SuperStar将模板分子（例如蛋白质结合位点）分解为与散点图中相对应的结构片段。然后将散点图叠加到模板的相应部分上，并转换为复合倾向图。SuperStar的原始版本完全基于CSD的散点图。在此，基于蛋白质-配体相互作用的散点图在SuperStar中得以实现，并在一组由122个蛋白质-配体复合物的X射线结构组成的测试集上进行了验证。在该验证中，倾向图与实验观察到的同类配体原子位置进行了比较。尽管小分子结构中的非键相互作用几何形状与蛋白质-配体复合物中的相似，但其相对出现频率不同。极性相互作用在第一类结构中更为常见，而疏水基团之间的相互作用在蛋白质晶体中更为常见。一般来说，基于PDB和CSD的SuperStar图在预测蛋白质-配体相互作用方面似乎同样成功。基于PDB的图更适合识别疏水口袋，并且内在地考虑了蛋白质原子位置的实验不确定性。如果已知组氨酸、天冬氨酸或谷氨酸蛋白质侧链的质子化状态，那么针对该质子化状态的特定基于CSD的图比代表质子化状态集合的基于PDB的图更受青睐。
