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• RMSD between two Ligands
  I have several docked conformations of one ligand docked to a receptor and I would like to calcul...
• What is the Ligand-RMSD meaning and calculation for peptide protein interaction?
  hello, I would like to know estimate the peptide binding site on the receptor. so i used the C...
• What about RMSD ?
  What about RMSD, how important is and where based it, how calculate rmsd. I use autodock vina, I ...
• Rmsd Check B/W Native Crystal Conformation And Docked Conformation
  Can anybody suggest tools for checking RMSD difference b/w docked ligand conformation and its nat...
• I'm predicting the protein-peptide structure. Why is the result different everytime?
  Hi. I am a doctoral student. The binding structure is predicted using specific protein and pept...
• Molecular Docking Parameters
  Hi guys, i'm performing docking using auto dock vina. But I've something problems. I'm doing do...
• What are the best ways to validate a docking result?
  I use autodock vina for docking. My prob. is how t validate a docking protocol. I know that I sho...
• How to chose best ligand option based on affinity and RMSD from Autodock vina docking results?
  Hi I have docked 20 ligands to a protein using Autodock vina (with 10 poses for each ligand). N...
• About the Align and RMSD in PyMol
  Hi everyone, I am currently working on calculating the RMSD between different protein struct...
• What does RMS in HEX represent?
  Dear All, I am a  new user of HEX and I have some confusions regarding the analysis of HEX dockin...
• Should energy minimization of native and mutant protein structures be done before RMSD calculation between these two?
  I want to calculate the RMSD values between a native protein and several of its mutant structures...
• Why Grid centers are different between Glide and ADTvina for the same Ligand-protein structures
  I am trying to conduct docking of couple of ligands on a protein using Glide and Autodock vina. ...
• Why Cluster Pdbs By Rmsd?
  I've been looking into RMSD clustering of PDBs, alot of my google searches just returns RMSD clus...
• RMSD of a structural superposition
  Hi, I am doing some structural comparisons with the visualization program Chimera to see similar...
• Energy minimization for hydrogen atoms only
  Hi, I am looking for a tool that optimizes the hydrogen-bond positioning in a protein-ligand com...
• Problem with Homology model- Ramachandram plot 89%. How to modify further
  I have done my homology model with a template of 33% sequence identity. That was the closest hit ...