DNA-binding is an important feature of proteins, and protein-DNA interaction involves in many life processes. Various computational methods have been developed to predict protein-DNA complex structures due to the difficulty of experimentally obtaining protein-DNA complex structures. However, prediction of protein-DNA complex is still a challenging problem compared with prediction of protein-RNA complex, this may be due to the large conformational changes between bound and unbound structure in both protein and DNA. We extend PRIME 2.0 to PRIME 2.0.1 to model protein-DNA complex structures. By comparing sequence and structure alignment methods, we found that structure-based methods can find more templates than sequence-based methods. The results of all-to-all structure alignments showed that DNA structure plays an important role in prediction of protein-DNA complex structure. By exploring the relationship of sequence and structure, we found that in protein-DNA interaction, numerous structures with dissimilar sequences have similar 3D structures and perform the similar function.

DNA结合是蛋白质的一个重要特征，蛋白质-DNA相互作用涉及许多生命过程。由于难以通过实验获得蛋白质-DNA 复合结构，因此已经开发出多种计算方法来预测蛋白质-DNA 复合结构。然而，与蛋白质-RNA复合物的预测相比，蛋白质-DNA复合物的预测仍然是一个具有挑战性的问题，这可能是由于蛋白质和DNA中结合和未结合结构之间的巨大构象变化。我们将 PRIME 2.0 扩展到 PRIME 2.0.1 以模拟蛋白质-DNA 复合结构。通过比较序列和结构比对方法，我们发现基于结构的方法比基于序列的方法可以找到更多的模板。all-to-all结构比对的结果表明，DNA结构在蛋白质-DNA复合物结构的预测中起着重要作用。通过探索序列和结构的关系，我们发现在蛋白质-DNA 相互作用中，许多具有不同序列的结构具有相似的 3D 结构并执行相似的功能。