BACKGROUND Analysis of preferred binding regions of a ligand on a protein is important for detecting cryptic binding pockets and improving the ligand selectivity. RESULT The enhanced sampling approach TAMD has been adapted to allow a ligand to unbind from its native binding site and explore the protein surface. This so-called re-TAMD procedure was then used to explore the interaction between the N terminal peptide of histone H3 and the YEATS domain. Depending on the length of the peptide, several regions of the protein surface were explored. The peptide conformations sampled during the re-TAMD correspond to peptide free diffusion around the protein surface. CONCLUSIONS The re-TAMD approach permitted to get information on the relative influence of different regions of the N terminal peptide of H3 on the interaction between H3 and YEATS.

中文翻译：

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re-TAMD：使用增强型采样探索H3肽与YEATS域之间的相互作用。

背景技术对蛋白质上的配体的优选结合区域的分析对于检测隐蔽的结合口袋和提高配体的选择性很重要。结果增强采样方法TAMD已被修改为允许配体与其天然结合位点解开并探索蛋白质表面。然后，使用这种所谓的re-TAMD方法来研究组蛋白H3的N末端肽与YEATS结构域之间的相互作用。根据肽的长度，探索了蛋白质表面的几个区域。在重新TAMD过程中采样的肽构象对应于围绕蛋白表面的无肽扩散。结论re-TAMD方法允许获得有关H3 N末端肽不同区域对H3与YEATS相互作用的相对影响的信息。