Laboratory of Chémoinformatics, UMR 7140, University of Strasbourg, France.
Comput Struct Biotechnol J. 2014 Jun 11;10(16):33-7. doi: 10.1016/j.csbj.2014.05.004. eCollection 2014 Jun.
We describe SILIRID (Simple Ligand-Receptor Interaction Descriptor), a novel fixed size descriptor characterizing protein-ligand interactions. SILIRID can be obtained from the binary interaction fingerprints (IFPs) by summing up the bits corresponding to identical amino acids. This results in a vector of 168 integer numbers corresponding to the product of the number of entries (20 amino acids and one cofactor) and 8 interaction types per amino acid (hydrophobic, aromatic face to face, aromatic edge to face, H-bond donated by the protein, H-bond donated by the ligand, ionic bond with protein cation and protein anion, and interaction with metal ion). Efficiency of SILIRID to distinguish different protein binding sites has been examined in similarity search in sc-PDB database, a druggable portion of the Protein Data Bank, using various protein-ligand complexes as queries. The performance of retrieval of structurally and evolutionary related classes of proteins was comparable to that of state-of-the-art approaches (ROC AUC ≈ 0.91). SILIRID can efficiently be used to visualize chemogenomic space covered by sc-PDB using Generative Topographic Mapping (GTM): sc-PDB SILIRID data form clusters corresponding to different protein types.
我们描述了 SILIRID（简单配体-受体相互作用描述符），这是一种新的固定大小描述符，用于描述蛋白质-配体相互作用。SILIRID 可以通过对对应相同氨基酸的位进行求和，从二进制相互作用指纹（IFP）中获得。这会产生一个由 168 个整数组成的向量，对应于项数（20 种氨基酸和一个辅因子）与每个氨基酸 8 种相互作用类型的乘积（疏水性、芳环面对面、芳环边对边、蛋白质供体氢键、配体供体氢键、与蛋白质阳离子和阴离子的离子键，以及与金属离子的相互作用）。通过在 sc-PDB 数据库（蛋白质数据库的可药用部分）中使用各种蛋白质-配体复合物作为查询进行相似性搜索，检查了 SILIRID 区分不同蛋白质结合位点的效率。检索具有结构和进化关系的蛋白质类别的性能与最先进的方法相当（ROC AUC≈0.91）。SILIRID 可以使用生成拓扑映射（GTM）有效地可视化 sc-PDB 覆盖的化学生物空间：sc-PDB SILIRID 数据形成对应于不同蛋白质类型的簇。
