Lee Hasup, Seok Chaok
Department of Chemistry, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 151-747, Republic of Korea.
Methods Mol Biol. 2017;1561:37-47. doi: 10.1007/978-1-4939-6798-8_4.
We introduce a web server called GalaxyPepDock that predicts protein-peptide interactions based on templates. With the continuously increasing size of the protein structure database, the probability of finding related proteins for templates is increasing. GalaxyPepDock takes a protein structure and a peptide sequence as input and returns protein-peptide complex structures as output. Templates for protein-peptide complex structures are selected from the structure database considering similarity to the target protein structure and to putative protein-peptide interactions as estimated by protein structure alignment and peptide sequence alignment. Complex structures are then built from the template structures by template-based modeling. By further structure refinement that performs energy-based optimization, structural aspects that are missing in the template structures or that are not compatible with the given protein and peptide are refined. During the refinement, flexibilities of both protein and peptide induced by binding are considered. The atomistic protein-peptide interactions predicted by GalaxyPepDock can offer important clues for designing new peptides with desired binding properties.
我们推出了一个名为GalaxyPepDock的网络服务器，它基于模板预测蛋白质-肽相互作用。随着蛋白质结构数据库规模的不断增大，为模板找到相关蛋白质的可能性也在增加。GalaxyPepDock将蛋白质结构和肽序列作为输入，并将蛋白质-肽复合物结构作为输出返回。蛋白质-肽复合物结构的模板是从结构数据库中选择的，同时考虑到与目标蛋白质结构的相似性以及通过蛋白质结构比对和肽序列比对估计的假定蛋白质-肽相互作用。然后通过基于模板的建模从模板结构构建复合物结构。通过执行基于能量优化的进一步结构优化，对模板结构中缺失的或与给定蛋白质和肽不兼容的结构方面进行优化。在优化过程中，考虑了由结合诱导的蛋白质和肽的灵活性。GalaxyPepDock预测的原子水平的蛋白质-肽相互作用可为设计具有所需结合特性的新肽提供重要线索。
