本文对来自PDB (Protein Data Bank)数据库的蛋白质-RNA复合物结构构建了非冗余非核糖体数据库(694个结构),并对此数据库统计了蛋白质和RNA序列及二级结构的界面偏好性.结果发现,蛋白质β折叠、310-helix和RNA未配对核苷酸,尤其是未配...本文对来自PDB (Protein Data Bank)数据库的蛋白质-RNA复合物结构构建了非冗余非核糖体数据库(694个结构),并对此数据库统计了蛋白质和RNA序列及二级结构的界面偏好性.结果发现,蛋白质β折叠、310-helix和RNA未配对核苷酸,尤其是未配对中空间排列不规整的核苷酸,具有显著的界面偏好性.据此,对二级结构进行归类,建立了考虑序列和二级结构信息的60×12氨基酸-核苷酸成对偏好势,并将其作为打分函数用于蛋白质-RNA对接中近天然结构的筛选.结果表明,该60×12统计势的打分成功率为65.77%,优于考虑蛋白质或RNA二级结构信息的统计势,及我们小组之前在251个结构上构建的60×8*统计势.该工作有助于加深对蛋白质-RNA特异性识别的理解,可推动复合物结构预测的进展.展开更多
A novel docking algorithm based on the geometric match is proposed for protein phage peptide complexes. The radii of gyration of protein phage peptide complexes are used as the criterion of geometric match on the inte...A novel docking algorithm based on the geometric match is proposed for protein phage peptide complexes. The radii of gyration of protein phage peptide complexes are used as the criterion of geometric match on the interface, which can be used to screen out the ligand structures with a good geometry fit without any prior description for the contact surface. The energy is evaluated for the structures with a good geometry fit. The algorithm is used to calculate the rigid and flexible docking of four protein phage peptide complexes and predict successfully the native like structures of phage peptides.展开更多
文摘本文对来自PDB (Protein Data Bank)数据库的蛋白质-RNA复合物结构构建了非冗余非核糖体数据库(694个结构),并对此数据库统计了蛋白质和RNA序列及二级结构的界面偏好性.结果发现,蛋白质β折叠、310-helix和RNA未配对核苷酸,尤其是未配对中空间排列不规整的核苷酸,具有显著的界面偏好性.据此,对二级结构进行归类,建立了考虑序列和二级结构信息的60×12氨基酸-核苷酸成对偏好势,并将其作为打分函数用于蛋白质-RNA对接中近天然结构的筛选.结果表明,该60×12统计势的打分成功率为65.77%,优于考虑蛋白质或RNA二级结构信息的统计势,及我们小组之前在251个结构上构建的60×8*统计势.该工作有助于加深对蛋白质-RNA特异性识别的理解,可推动复合物结构预测的进展.
文摘A novel docking algorithm based on the geometric match is proposed for protein phage peptide complexes. The radii of gyration of protein phage peptide complexes are used as the criterion of geometric match on the interface, which can be used to screen out the ligand structures with a good geometry fit without any prior description for the contact surface. The energy is evaluated for the structures with a good geometry fit. The algorithm is used to calculate the rigid and flexible docking of four protein phage peptide complexes and predict successfully the native like structures of phage peptides.