Konc Janez, Janezic Dusanka
National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia.
J Chem Inf Model. 2007 May-Jun;47(3):940-4. doi: 10.1021/ci6005257. Epub 2007 Mar 28.
A new algorithm to predict protein-protein binding sites using conservation of both protein surface structure and physical-chemical properties in structurally similar proteins is developed. Binding-site residues in proteins are known to be more conserved than the rest of the surface, and finding local surface similarities by comparing a protein to its structural neighbors can potentially reveal the location of binding sites on this protein. This approach, which has previously been used to predict binding sites for small ligands, is now extended to predict protein-protein binding sites. Examples of binding-site predictions for a set of proteins, which have previously been studied for sequence conservation in protein-protein interfaces, are given. The predicted binding sites and the actual binding sites are in good agreement. Our algorithm for finding conserved surface structures in a set of similar proteins is a useful tool for the prediction of protein-protein binding sites.
开发了一种新算法，该算法利用结构相似蛋白质中蛋白质表面结构和物理化学性质的保守性来预测蛋白质-蛋白质结合位点。已知蛋白质中的结合位点残基比表面的其他部分更保守，通过将一种蛋白质与其结构邻居进行比较来发现局部表面相似性，有可能揭示该蛋白质上结合位点的位置。这种方法以前曾用于预测小分子配体的结合位点，现在扩展到预测蛋白质-蛋白质结合位点。给出了一组蛋白质的结合位点预测示例，这些蛋白质此前已针对蛋白质-蛋白质界面中的序列保守性进行过研究。预测的结合位点与实际结合位点吻合良好。我们用于在一组相似蛋白质中寻找保守表面结构的算法是预测蛋白质-蛋白质结合位点的有用工具。
