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• Hydrogen Bonded And Non-Hydrogen Bonded Pairs Using Dssp
  HI I want to know how can I find the hydrogen-bonded and non-hydrogen bonded pairs of a beta-hai...
• Tools To Visualize Hydrogen Bondings Between Two Different Binding Proteins?
  I'm studying the interaction between two binding proteins (two chains) using Rasmol but it only s...
• How to calculate hydrogen bonds of a protein structure from its pdb file?
  Hello every body. My question might seem very basic so excuse me about that. I need to calculate...
• Non-bonded atoms in PDB
  i have generated protein model using PHYRE2. i need to use it for docking on AutoDock Tools. Whil...
• Java api or library to calculate hydrogen bonds of a protein
  Hello every body. I need a Java api or library for calculating hydrogen bonds of a given pdb fil...
• How To Add Bond Between Metal Atom And Coordinated Water Molecule?
  Hi everyone, I'm new to AutoDock and I currently involved in a protein-ligand docking study. My...
• Why Still A Hydrogen Bond Between A Mutated Ligand And The Protein?
  Normally, when there is a mutation on the residue of a ligand, it causes the folding to change. T...
• How Calculate The Energy Contribution Of Interactions In A Protein ?
  Hello everyone, I would like to calculate the energy contribution of interactions in a protein. ...
• Software For Hydrogen Bond Detection In Pdb Data?
  In order to study the network structure of proteins, I'm looking for software that can predict th...
• hydrogen bonds in a pdb file through gromacs
  Can I use gromacs to calculate hydrogen bonds within a single pdb file? I do not have a tpr file.
• Energy minimization for hydrogen atoms only
  Hi, I am looking for a tool that optimizes the hydrogen-bond positioning in a protein-ligand com...
• Protein-Protein Complex Hydrogen Bonding
  Hi i have docked two proteins using grammax. The 3D structure that I am studying is forming one...
• How to detect entire beta sheet (multiple strands) using STRIDE on a pdb file?
  In PDB files, the header lists the beta **sheets** and then the **strands** in those sheets. I pr...
• Dssp And 6 Different Hydrogen Bonds - What Are They Exactly
  DSSP returns 6 different hydrogen bonds. HYDROGEN BONDS OF TYPE O(I)-->H-N(J) ; PER 100 RESI...
• Could It Be Possible To Define Hydrogen Bond With A Particular Residue In Docking??
  Hello, I was wondering that is it possible to defined hydrogen bonding of ligands with a particu...
• AutoDock 4 result analysis
  When a receptor is coupled to a ligand, every time when the molecule is docked with AutoDock prog...