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Is there a computer program that simulates biology on a molecular level? Software that has rules that simulates the rules of molecular-biology?

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What do you mean by "simulates biology on a molecular level"? There are definitely 3D molecule viewers, as well as programs for organic chemistry mechanisms, but not something that encompasses every detail of all living processes ever. –  LanceLafontaine Aug 10 '12 at 1:36

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There is a recent paper that introduced the first molecular-level whole-cell simulation.

Karr, J.R., Sanghvi, J.C., Macklin, D.N., Gutschow, M.V., Jacobs, J.M., Bolival, B., Assad-Garcia, N., Glass, J.I., & Covert, M.W. (2012). A whole-cell computational model predicts phenotype from genotype. Cell 150:389-401 DOI: 10.1016/j.cell.2012.05.044

The authors combined 28 different sub-modules of various biological processes from the literature. Each one operates at the level of macromolecules, although models them in different ways: some by ODEs, some by logic; some by agent-based approaches. If you want to fool around their code is available online and I wrote a basic introduction/summary of the paper.

Here are some related bio.SE questions motivated by that model:

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Just a very important note, seen what the OP is asking. Simulating one cell is great, but it does not in any way mean that we can currently simulate an entire organism with that same level of detail. –  nico Oct 16 '12 at 17:41

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