How to start a docking project? | 4 Practical tips PART 2

Molecular docking seems deceivingly simple at first glance, but several computational chemistry factors can influence the quality of the final result. Anyone who is research naive can generate both revolutionary results and artifacts, unrealistic results without realizing.
Force field parameters are implemented in Molecular mechanics (MM) methods, as part of Potential energy function and in more simplified ways in docking scoring functions. The total potential, usually does not differ very much from one force field to another. The force fields usually vary between one each other based on the parameterization. However, the potential energies calculated in docking methods, can vary significantly from one method to another, since several approximations are applied. Scoring functions enforced in docking programs make various presumptions and simplifications and so they do not fully account for physical phenomena such as, desolvation upon ligand binding, or entropic effects. In docking, the scoring function attempts to estimate and quantify the fit of a ligand into the binding site. The quantification and the ranking of the predicted ligand conformations is a crucial to be able to interpret the docking results. This process is essential to be able to ultimately differentiate correct poses from incorrect ones, but also to identify correct binders in case of a computational virtual screening. Thus, the development of reliable scoring functions is of central importance.
B-factors in PDB files commonly are seen as a measure of (local) mobility in the (macro)molecule, but this value is is strong relation with the correctness of the structure and resolution as well.
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[@angelina5285]

I like that you speak clear and to the point! Please make more videos!

[@uppumanesh5767]

Finally there is someone to explain these things in a simple way👌👌

[@scienceaddicted3431]

These comments always motivate me. I have been very busy in my day job, but i have some videos planned

[@scienceaddicted3431]

Feedback and questions are welcome. Please check out Part 1 of the Docking practical tips , for a full picture of the topic

[@yaseenjanalchemist8026]

Check my dear and near mam quite simple simple explanation that’s really amazing

[@scienceaddicted3431]

Continued with the practical tips for docking. For more information about force field, please read the description. I wrote there a more extensive explanation.

[@uppumanesh5767]

Expecting many more videos from the channel.. thank you..

[@scienceaddicted3431]

Thanks for your nice comment! I will make everything possible to continue

[@TrangNguyen-lv1lc]

Thank you. It is helpful

[@TheFailsPlays]

Great Intro! thank you so much and please keep theese coming!

[@scienceaddicted3431]

Thank you! I plan to continue, and do my best to post every other week. The comments keep me motivated. 😉

[@yaseenjanalchemist8026]

@@scienceaddicted3431 haha sooo nice of yiu

[@nikitabaraboshkin7415]

All docking studies must be approved by MD simulation.

[@yaseenjanalchemist8026]

Let me learn docking techniques from you 🥰🥰🥰 start from now

[@chowdhurylutfunnahar1290]

Thank you so much for clearance

[@scienceaddicted3431]

Thanks for watching! Glad to hear you found it useful

[@yaseenjanalchemist8026]

How do I can get this materials or in other words can I use your vido for my presentation What I mean is that to aware the students from this technology