![]() In the above situation, POVME can perform two useful tasks: How does POVME enable better drug design? POVME3 is primarily intended to solve this problem of making molecular dynamics simulations more useful to drug designers. ![]() Sometimes, a scientist will do a simulation and end up with hundreds of thousands of snapshots (each a single protein structure), and it is impractical to dock to all of them. However, even moderately effective docking is computationally expensive. In other words, conclusions like “The RMSD went up” do not tell us why people get cancer or what to do about it.Įveryone does simulations different ways and for different specific reasons, but I’d argue that the most directly valuable question that people can try to answer is “how does this simulation help me make a drug?” The normal way for people to use a protein structure to make a drug is by using “docking” software, which tells them how likely a given small molecule is to fit into a binding site. ![]() There are a growing number of tools that try to quantitatively answer the question of “what in the world just happened in this simulation”, but they often do abstract analyses with no clear actionable output. However, what usually happens is that scientists run simulations (at great computational cost), and then see a big protein wiggling around, and have no idea what to do with it. Molecular Dynamics simulations are getting really popular in our field of science. Gcq#395: “It was something to at least have a choice of nightmares” (Joseph Conrad) Please don’t hesitate to complain - The problems that give you the hardest time are the ones I’ll focus on fixing first! You can expect far less stability and user-friendliness from this software than you could from things like VMD. I also have two other essentially full-time projects. Jeff’s note: I am the current lead developer of POVME.
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