I have docked two proteins using patchdock but i am not able to view the P-P interaction in PIC calculator. I doubt there must be something wrong with the PDB files that i have given as input. Please suggest what to do?
I am attaching the complex PDB + Individual proteins.
PDB files are ok I think. Do you add polar hydrogens before performing docking?? if not, then give it a try by adding polar hydrogens. Best of luck.
PatchDock often messes with the structure. Try refining the PatchDock output in FireDock. I would also suggest you to rename the chain in one of the proteins as chain B. In the complex both the proteins chains are named as chain A, which might be the reason why you are unable to view the protein protein interactions.
Both components have the same chain label in your complex (chain A). Most protein analysis programs run eventually into problems if your pdb file contains multiple residues that have both the same residue number and the same chain label. Try again with the attached file (I selected the second protein and replaced " A " by " B " in a text editor)
@Uttam Pal : Sir, I did refine the output file with firedock but the problem still persists. I'll try once by renaming the chains . I had earlier docked files earlier with same chain names but i did not face any such problem.
@Mokhtar Nosrati: I thought the same but i docked it again with minimized structure. I don't have any idea how accurate is energy minimization in Swiss PDB viewer but i will git it a try with Maestro.
At least PROTEIN-PROTEIN INTERACTIONS works fine on the PIC calculator after I replaced the chain label (and the server specifies that: * This option can accept only a multichain protein file.) Other Options, such as INTRAPROTEIN INTERACTIONS will probably work with a single chain label, though the output may not make sense, since you cannot tell which residue is meant if two residues have the same name, label and sequence, for the others you might at least be able to tell by sequence, residue type. Try with the corrected file I sent you, and let me know which calculations still cause problems!
@Uttam Pal : Thank you sir, renaming the chains helped.
@ Annemarie Honegger: Mam,all the calculations work fine now. Thank you so much for taking time out of your schedule and doing the correction.
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools