论文标题
蛋白质的构象变异性与单链DNA结合：新的对接视角的新基准
Conformational variability in proteins bound to single-stranded DNA: a new benchmark for new docking perspectives
论文作者
论文摘要
我们探索了蛋白质数据库（PDB），以收集蛋白质-SSDNA结构，并创建一个多构成对接基准，包括结合和未结合的蛋白质结构。由于ssDNA高柔韧性，当不结合时，基准中不包含ssDNA未结构的结构。对于被鉴定为同一蛋白质的边界解体结构的91个序列认同组，我们研究了由ssDNA结合诱导的蛋白质的构象变化。此外，基于某些组的几种结合或未结合的蛋白质结构，我们还评估了绑定或未结合条件下的内在构象变异性，并将其与所谓的结合诱导的修饰进行了比较。为了说明此基准测试的用例，我们使用吸引对接软件进行了对接实验。据我们所知，这种基准是第一个在这样的程度上仔细研究ssDNA-蛋白质相互作用的可用结构的基准，旨在改善专门用于这种分子相互作用的计算对接工具。
We explored the Protein DataBank (PDB) to collect protein-ssDNA structures and create a multiconformational docking benchmark including both bound and unbound protein structures. Due to ssDNA high flexibility when not bound, no ssDNA unbound structure is included in the benchmark. For the 91 sequence-identity groups identified as bound-unbound structures of the same protein, we studied the conformational changes in the protein induced by the ssDNA binding. Moreover, based on several bound or unbound protein structures in some groups, we also assessed the intrinsic conformational variability in either bound or unbound conditions, and compared it to the supposedly binding-induced modifications. To illustrate a use case of this benchmark, we performed docking experiments using ATTRACT docking software. This benchmark is, to our knowledge, the first one made to peruse available structures of ssDNA-protein interactions to such an extent, aiming to improve computational docking tools dedicated to this kind of molecular interactions.
