Hello, what web server protein refinement tool can you recommend? I tried to use Galaxy Refine, but HADDOCK does not accept refined PDB. “ATOM/HETATM line does not meet the expected format” this is what pops up every time I use the refined PDB in HADDOCK.
Hi! you may want to check out the HADDOCK refinement interface
Hello, HADDOCK refinement interface removes my protein bad angles and bonds. However, it does not improve my Ramachandran analysis result.
It is only a very short refinement… No miracles.
Check our article about refining complexes to get an idea of what can be done / achieved.
- T Neijenhuis, S.C. van Keulen and A.M.J.J. Bonvin. Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4. Structure 30, 476-484 (2022).