what does it mean. will it affect my docking results. if it affects how to prevent them ??
As we all know, the Discovery studio 4.5 client for docking is virtual, calculating based on database.
some unfavourable steric bumps mabe represent that the main influencing factors of molecular binding energy, make ligands and receptors not so stable, you can use the GROMACS to stimulate the molecular dynamics to more comprehensive analysis. i hope this can help you, good luck!
It means that the model is not a perfect imitation of the real structure.
Before docking you must minimize the energy and torsional strain of both protein i.e. bring protein and ligand to minimum energy state or most stable state which can be done via Swiss pdb viewer and AVOGADRO. After minimizing the energy and strain go for docking in the drug screening section Use iGEMDOCK for offline and better screening. Steric bumps are due unstable structure and maximum torsional strain
Docking algorithms use softened van der Waals radii to enable a faster compound placement. So it is ok if ligand-protein distances may be a little shorter than they should be.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology