I would like to work on designing a peptide that works at the interface of two protein that interact with each other thus inhibiting this interaction.
docking doesnt required forcefield till u will go for molecular dynamics and simulation....
Yes but is it really necessary to do molecular dynamics studies/ most of the papers i have read so far have done molecular dynamic studies
yes it is always good to go for MD simulation after getting potent inhibitor so that mechanism of inhibition and interaction among these partner can be justified..
Thank you! I cant work with MDs as i am a novice in it and these software for MDs are not freely available
it is not manditadory to do MD studies always. if the protein is collected from pdb database then u can go for docking studies. but if it is modelled protein it is necessary as all the modelling softwares are not perfect. NAMD/VMD is the best software for MD studies perticularly researchers
what would you suggest if the protein of interest has PDB entry bound to a ligand.
That depends on your purpose of your project. If you want to develop a new strategy for design a novel pep tide to inhibit protein-protein interface. IT is necessary for you to work on building an effective force filed for protein-peptide interaction.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Biomolecules
- Peptides