I would like to study the binding of different aptamers (RNA sequences) to the ligand PFOA. Haddock allows me to do so, but I don’t know how to tune the parameters to optimize the results, and cannot find any information anywhere. I would really appreciate if someone could give me some notions about how to find the best parameters to perform Haddock in this case. Thanks!
Wee never benchmarked RNA-ligand docking but did some yet unpublished work on DNA-ligand modelling. Here is a matrix of parameters (the last column should work for RNA-ligand modelling):
|default value||Protein/Small molecule||Protein/DNA||DNA/small molecule|
|Dieletric constant for it0||dielec_0||rdie||cdie||rdie||cdie|
|Dieletric constant for it1||dielec_1||rdie||cdie||rdie||cdie|
|MD steps for rigid body high temperature TAD||initiosteps||500||0||500||0|
|MD steps during first rigid body cooling stage||cool1_steps||500||0||500||0|
|Initial temperature for second TAD cooling step with flexible side-chain at the interface||tadinit2_t||1000||500||1000||500|
|Initial temperature for third TAD cooling step with fully flexible interface||tadinit3_t||1000||300||1000||300|
|Weight of the intermolecular van der Waals energy for scoring at the rigid-body docking stage||w_vdw_0||0.01||1||0.01||1|
|Weight of the intermolecular electrostatic energy for scoring at the final stage||w_elec_2||0.2||0.1||0.2||0.1|
|Dielectric constant for rigid-body docking||epsilon_0||10||10||78||78|
|Dielectric constant for the semi-flexible refinement||epsilon_1||10||10||78||10|
And in addition you might consider setting the weight of the desolation energy term in the scoring function to 0
Thank you so much!