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I'm learning biology on my own and it's pretty hard to understand all processes inside a cell from the side of chemistry and physics and in some cases pointless to bring a complexity instead of abstraction.

I just curious to know if we have some open-source projects that provide 3D program models of a cell? I mean not just like study model that shows cell organelles and their names but I want something that shows real cellular processes like (1x1 or close to it) real model of a living (in program) cell with some types of abstraction levels.

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    $\begingroup$ I don't know of such resources but certainly there are good animated videos of different cellular processes. Khan Academy would be a nice place to look for video tutorials. I also would want to add that a full computational model of an entire cell would be quite complex and I haven't come across any (the closest to complete was that of M.genitalium and it was not intended as an educational resource but a research project instead). $\endgroup$ – WYSIWYG Feb 25 at 12:50
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Not of a complete cell, that would seriously overload even most powerful animation software/hardware you could build, not to mention there are gaps in our understanding of the cell. Understanding a cell purely through chemistry is possible if a bit masochistic, sooner or later you are going to need to approach it from a different direction to get the whole picture. There is so much complexity in a modern cell that sooner or later you have to start looking at the emergent characteristics. Don't believe me check out this chart of just the common metabolic pathways in a human cell, you are looking a 3.5 billions years of kluges, breathtaking elegance, rube goldberg monstrosities, and duck tape solutions all layered and tangled into each other, messy doesn't begin to describe it.

But there is several places creating models of individual processes, modeling each individual atom. These will let you at least understand hte chemistry of the components.

www.dnalc.org is focused on nucleic acids and their interactions.

Their work is related to Harvard's biovisions program which uses XVIVO. which is a much rougher but larger scale approach and may be the closest to what you want.

Cambridge MRC has a more diverse selection with better visualization of the actual chemical interactions.

Swissmodel by the Swiss Institute of bioinformatics focuses on protein modeling and has a free to use program and database.

There is even a wikipedia database Protepedia

Image from www.dnalc.org animation

enter image description here

I'm sure others on the site could list a dozen other such programs/databases.

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    $\begingroup$ @user237650 Thank you, that should have fixed it. $\endgroup$ – John Feb 28 at 2:26
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The complete function of a cell is something which is still quite beyond our current knowledge and understanding. Many gaps remain that prevent us from building such a complete model, and also from engineering an artificial object that would reproduce some basic function of a living cell.

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