Simulations after docking are not "necessary" in the sense that one absolutely must run MD, but the process can be helpful depending on the question you're trying to answer. An assessment of protein-ligand complex stability is one example where running simulations on a docked complex would be necessary. Per Angana's comment, building an ensemble of structures/conformations is another excellent example. The programs mentioned by the others are great free software options.
Regarding water as a solvent, you don't have to use water (again depending on the question you're trying to answer), but water is most commonly used. Water with ions in MD are analogous to assays where an aqueous solution (salt in water, buffers, etc) is used to perform some assessment. So running a simulation in a water box with ions added will give you a decent approximation (depending on your parameters) of what you would see in a wet lab situation.
I hope this helps.
Since its docking, I consider u are dealing with biological molecules like protein, DNA or RNA. Hence, it is logical to use water as a solvent coz that would mimic the biological conditions to a better extent. U can add ions to neutralize ur molecule or attain a bilogically significan concentration. It is good to do simulation after docking coz that would give u an ensemble of structures which are possible after docking and u can draw up ur conclusion from the quilibrated structures. Hope Im clear.
Angana
because water is the natural solvent in a living system. to mimic the life environment in computationally, we are using water as a solvent. moreover, we often use to change the solvent, the choice is depend upon the natural environment of protein inside the living system.
After docking you need to equilibrate the system in adequate environment (water).
Norbert
molecular dynamic simulation means that the complex is stable . so it's used in validation of the docking . And as the time of production increase as means higher stability .
GROMACS is easy to use. But NAMD, CHARMM nd AMBER are also good. One has to choose the forcefield properly
Simulations after docking are not "necessary" in the sense that one absolutely must run MD, but the process can be helpful depending on the question you're trying to answer. An assessment of protein-ligand complex stability is one example where running simulations on a docked complex would be necessary. Per Angana's comment, building an ensemble of structures/conformations is another excellent example. The programs mentioned by the others are great free software options.
Regarding water as a solvent, you don't have to use water (again depending on the question you're trying to answer), but water is most commonly used. Water with ions in MD are analogous to assays where an aqueous solution (salt in water, buffers, etc) is used to perform some assessment. So running a simulation in a water box with ions added will give you a decent approximation (depending on your parameters) of what you would see in a wet lab situation.
I hope this helps.
In addition to what Stephanie mentioned clearly, MD simulations (in water + ions) may be used to answer questions related to the binding free energies quantitatively more accurately since the MD force fields are more accurate. The scoring functions that you get from docking may not always give the right relative contribution of each contact between ligand and receptor; for example when you compare scoring functions for different ligands to the same receptor, the ligand with larger number of contacts may have higher score, which may not always be true. In addition, sometimes you may be interested in the role of the water to the binding strength which are close to the binding site.
"...why is water used as a solvent for simulations"
Yeah... in silico world in action... :-)
How else? Biopolymers exist in water solutions both in vivo and in vitro. If you dry out a cell, it will not be alive any more. If you put DNA in a non-aqeous environment, it will commit a suicide and break down. Life exists in water.
After docking you have possible candidates, you do need to perform simulations to find out if the candidate is suitable. The whole docking story is actually serving to eliminate the very unprobable candidates and to concentrate the further studies (simulations afterwards, chemical in vitro studies in the lab, etc...) on the most probable candidates. Blindly applying docking is a road to nowhere and has nothing to do with natural science.
The stability of the ligand is given by the estimated free energy. This energy involves the contribution of the solvation free energy that is crucial to the stability of the non-polar groups. The entropic contributions are most relevant for this type of problem.
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology