So I am working on 3D structure prediction for some proteins and need to validate the structure using amongst others a tool that does Ramachandran plot. Any ideas about possible tools?
There are several web based and local software tools that can generate Ramachandran plots. To name a few: WHATCHECK PROCHECK, MolProbity, PDBSum, VMD, Chimera, SWISS PDB Viewer, Free Maestro (Schrodinger) etc.
You can use UCLA-DOE LAB — SAVES v6.0 (https://saves.mbi.ucla.edu/). It is a server that makes an evaluation of the 3D structure of proteins using 5 different servers: WHATCHEK, Procheck, Errat, Verify 3D and Prove. The first one makes an evaluation using the Ramachandran plot analyses
There are several tools that could be used, I would recommend Ramachandran Server for structures deposited in the PDB, based on MOLEMAN2 by Gerard Kleywegt; STAN Server which will accept any PDB file you provide, also based on MOLEMAN2; MolProbity from the Richardson laboratory at Duke University, which is used on the PDB website itself; and RAMPAGE. Please visit https://warwick.ac.uk/fac/sci/moac/people/students/peter_cock/python/ramachandran/other/ for a complete description.