Bound vs unbound molecular docking A protein's conformation is categorised into bound (complex) and unbound (one outside of a complex) structures (Figure ). The bound docking separates a complex and then redocks parts of the complex to build the original complex. While bound docking is essential for developing new docking programs, it does not hold much value in biology. When an unbound docking program predicts a new interaction between a ligand and target (where the ligand and target are not already bonded), it enhances our understanding and becomes highly beneficial. Bound (in green) and unbound (in red) TF-DNA docking test case construction proceeds to assess docking performance methodically. The bound complex is broken into two binding components: TF and DNA. These elements then are employed for docking, sometimes known as "bound docking," which usually leads to better outcomes on validation sets because of their pre-existing interface compatibility. This method might not, however, fairly depict real-world conditions in which the bound conformation is not always accessible. "Unbound docking" is exploited to overcome this restriction, whereby molecular docking uses the unbound TF, as shown in red. Under this situation, the unbound TF lacks a pre-formed interface fit for complexing with DNA. Hence, flexibility is needed to enhance docking performance. This adaptability enables conformational changes, raising the possibility of effective docking in useful contexts. Comparative bound and unbound docking approaches help one understand the need for structural adaptation to reach precise TF-DNA interactions ( ).