Tag
Protein Structure Validation
Molecular Modeling How to Read a wwPDB Validation Report Before You Dock Read the percentile sliders, clashscore, RSRZ and ligand RSCC in a wwPDB validation report, then pick the best PDB entry to dock… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling SAVES Server Tutorial: ERRAT, Verify3D and PROCHECK Upload a homology or AlphaFold model to SAVES v6.1 and learn to read ERRAT, Verify3D and PROCHECK scores. Check your model before… Dr. Abdul Rajjak Shaikh 13 min read Molecular Modeling Ramachandran Plot from a GROMACS Trajectory (gmx rama) Learn to run gmx rama on an MD trajectory, plot every frame as a phi/psi density in Python, and spot residues that… Dr. Abdul Rajjak Shaikh 14 min read Molecular Modeling How to Validate a Protein Structure: Ramachandran Plots and MolProbity Scores Explained Validate your AlphaFold or homology model with a Ramachandran plot and MolProbity before you waste compute on docking. Learn every score and… Dr. Abdul Rajjak Shaikh 10 min read Updated