If you are familiar with MD packages you apply constraint on the structure (except the part which you believe it is random coil) and heat up the system to obtain random coil.

Please make a note that for protein docking, random coil will not give you a reliable result. Moreover, check the disorder profile/pattern for a-synuclein. Disordered proteins or regions are different from random coil. Again repeating the earlier point, docking with such regions is not advisable as they will not yield reliable data

the above two points are true, first constrain you can obtain the obtain random coil region, then, if you want a more reliable study of the interaction would be advisable to perform more robust studies, such as FEP or MM-GBSA.

Thank you all for your answers and suggestions!

check this link. I have provided the answer to this in the link given below. you just need to assign the phi/psi values of coil (180/180).

https://www.researchgate.net/post/How_can_I_make_a_PDB_file_from_a_predicted_secondary_structure_for_a_protein

good suggestion but it will not help as synuclein is a disordered protein.Assigning false phi/psi angles will be altering the native orientation. Look out for molecular recognition features.These areas have high propensity to undergo disorder to order transition. Selecting such region would be more preferable and provide relatively accurate data.

Hi Dev,

You can use Molefacture plugin of VMD to generate random coil.

Here is the link: http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/

PS: I think its kind of late reply but for future reference.