Hi Akhileshwar,

In general protein-ligand interaction, we estimate the binding affinity of ligand based on Dock score, Energy, residual interaction (Hbond, vdw, steric) with distance (Ao).

In Swiss dock, After getting the result file (.rar file (score, docked molecule named as clusters.dock4, target)) you need to do analyse the interaction using UCSF Chimera software.

Just to do the steps in Chimera

File > Open , then load target.pdb

Tools > Surface/Binding Analysis > ViewDock, choose clusters.dock4.pdb (Dock 4, 5 or 6 format).

Find the best residual interaction such as Hbond, vdw in conserved sites of protein based on Energy, Full fitness. Find a good interaction by comparing with the standard complex structures substrates (ligands) or different protein docking results with a same ligand.

Hope this information is useful for you. 

Can someone help me with the interpretation of results obtained by docking study (SwissDock)? - ResearchGate. Available from: https://www.researchgate.net/post/Can_someone_help_me_with_the_interpretation_of_results_obtained_by_docking_study_SwissDock#5877926948954c5d31142d55 [accessed Jan 12, 2017].

Hi, this link will be useful for you,

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

Hi Akhileshwar,

In general protein-ligand interaction, we estimate the binding affinity of ligand based on Dock score, Energy, residual interaction (Hbond, vdw, steric) with distance (Ao).

In Swiss dock, After getting the result file (.rar file (score, docked molecule named as clusters.dock4, target)) you need to do analyse the interaction using UCSF Chimera software.

Just to do the steps in Chimera

File > Open , then load target.pdb

Tools > Surface/Binding Analysis > ViewDock, choose clusters.dock4.pdb (Dock 4, 5 or 6 format).

Find the best residual interaction such as Hbond, vdw in conserved sites of protein based on Energy, Full fitness. Find a good interaction by comparing with the standard complex structures substrates (ligands) or different protein docking results with a same ligand.

Hope this information is useful for you. 

Can someone help me with the interpretation of results obtained by docking study (SwissDock)? - ResearchGate. Available from: https://www.researchgate.net/post/Can_someone_help_me_with_the_interpretation_of_results_obtained_by_docking_study_SwissDock#5877926948954c5d31142d55 [accessed Jan 12, 2017].