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Ligand Viewer is a 2D Visualiser that allows you to EFFICIENTLY, QUICKLY and EASILY analyse the interactions and placement of small molecules bound to a protein.
You have access to a variety of details such as all close side chains, all close hydrogen bonds, a customisable xyz plane, and side chain highlighting to make it easy to visualise how each molecule fits into a protein.
+ LV can read 3D molecular file formats MDL, sdf, sd and the Protein Data Bank format PDB
+ For each molecule, you can view its properties that are stored in the sd/sdf file and easily compare binding poses
User Guide
Side Chains
Highlighting:
Highlight side chains by clicking on them. This centres them on the screen and recalculates their position so that the highlighted side chains don't move when switching between each ligand. This allows the user to locate the same side chain(s) that are common amongst the ligands, or that are important for binding. This makes it easy to compare binding modes.
Position:
Unhighlighted (grey or yellow) - The position is the average position of all protein atoms within the same residue that are within the specified range of the ligand [the range can be changed in the preferences].
Highlighted - The position is the average position of all side chains with the same name that are common among each ligand.
Side chain colours:
Grey - Standard side chain
Yellow - A side chain that is common amongst all ligands
Brown - A side chain that is outside of the standard specified range from the ligand, but inside the specified range for hydrogen bonds (i.e. the range for hydrogen bonds must be larger than the standard range)
Other - A highlighted side chain [highlighting colour can be changed in the preferences]
Hydrogen Bonds
All atoms of the protein that are within the specified range for hydrogen bonds [the range can be changed in the preferences] are tested to see if they form a hydrogen bond. Only hydrogen bonds containing oxygen or nitrogen atoms are shown.
Molecule Details Window
To access all the information provided in the sd/sdf file for the ligand, open the molecule details window which can found under the File menu.
Side Chains
Highlighting:
Highlight side chains by clicking on them. This centres them on the screen and recalculates their position so that the highlighted side chains don't move when switching between each ligand. This allows the user to locate the same side chain(s) that are common amongst the ligands, or that are important for binding. This makes it easy to compare binding modes.
Position:
Unhighlighted (grey or yellow) - The position is the average position of all protein atoms within the same residue that are within the specified range of the ligand [the range can be changed in the preferences].
Highlighted - The position is the average position of all side chains with the same name that are common among each ligand.
Side chain colours:
Grey - Standard side chain
Yellow - A side chain that is common amongst all ligands
Brown - A side chain that is outside of the standard specified range from the ligand, but inside the specified range for hydrogen bonds (i.e. the range for hydrogen bonds must be larger than the standard range)
Other - A highlighted side chain [highlighting colour can be changed in the preferences]
Hydrogen Bonds
All atoms of the protein that are within the specified range for hydrogen bonds [the range can be changed in the preferences] are tested to see if they form a hydrogen bond. Only hydrogen bonds containing oxygen or nitrogen atoms are shown.
Molecule Details Window
To access all the information provided in the sd/sdf file for the ligand, open the molecule details window which can found under the File menu.
