Simulating Drug interactions with Proteins?

[khunter]

Can Folding@home simulate Drug interactions with Proteins?

[susato]

Hello khunter and welcome to the forum!

F@H can indeed simulate drug-protein interactions. The molecular dynamics calculations behind F@H can apply to interactions between any molecules. The simulations with "explicit solvent" include interactions between protein and the surrounding water and urea molecules. Simulations of the p53 tumor suppressor address the aggregation of two and four proteins. And Project 2142 simulates the interactions between the aldose reductase protein and two small drug-size molecules.

Poke around on the project description pagesand you'll see the entire range of problems addressed by F@H so far.

[VijayPande]

Can Folding@home simulate Drug interactions with Proteins?

Yes (and in fact we have done and already published papers on this). We are getting more and more interested in drug-target interactions in general, especially for predicting the toxicity of new drugs.

[khunter]

Therefore would Folding@home be able to simulate how certain drugs work?

For example, when Adderall (amphetamine) is taken with Clonazepam (benzodiazepine), what happens?

Specifically to the below protiens:

Code: Select all

norepinephrine transporter (NET) protein: http://www.expasy.org/uniprot/P23975

dopamine transporter (DAT) protien: http://www.expasy.org/uniprot/Q01959

serotonin transporter (SERT) protien: http://www.expasy.org/uniprot/P31645

[folding4u]

I think that we don't need much more data on those drugs. They are old and need to be replaced with something better and that's where research should be focused.

[pluto7777]

They are old and need to be replaced with something better and that's where research should be focused.

Are we talking about batteries or drugs?

[folding4u]

Does FAH research have applications in batteries as well?

[codysluder]

Does FAH research have applications in batteries as well?

I think it was a joke. Generally speaking reactions in batteries are inorganic and do not depend on the precise shape of any proteins.

See http://folding.stanford.edu/English/Science

[pluto7777]

Does FAH research have applications in batteries as well?

Sorry that was a lame joke. I wholly agree Folding@home should focus on new drugs, but there's no need to toss out old ones if they still work.

[folding4u]

I realised it was a joke, but I would have given it more weight if I had suggested scrapping old drugs.

I do think differently on whether the amphetamines work or not. People think there might be brain damage from longer use, etc. For me that is not 'working'.

[susato]

Getting back to khunter's question, that's a better question for a doctor than for the F@H project, especially since the body develops tolerance to drugs like these, especially the benzodiazepenes, where the side effects mount up as the therapeutic effects decline. There must be more going on in that system than just a single intact small molecule, and neurotransmitters, binding competitively to one or more of the proteins you mentioned.

[spazzychalk]

I wholly agree Folding@home should focus on new drugs

free research for the evil pharma industries? its enough in concept to make me stop folding.

[codysluder]

I wholly agree Folding@home should focus on new drugs

free research for the evil pharma industries? its enough in concept to make me stop folding.

FAH should continue to focus on basic science and continue to publish the results for anybody to use.

Big pharma is like any business, focuses on making money. That doesn't make them inherently evil, but they're not inherently good, either, but more accurately neither. We need them to make new drugs that can cure disease, but we do not need our donations used to benefit one company over another, but rather give them a better opportunity to compete to see who can use the our results most quickly and most effectively.

[spazzychalk]

please.. they havent cured anything since polio. in my world there are only 2 kinds of drugs -1 the good drug you take for a while it fixes it and thats it. 2 the bad drug you take forever. its extortion inherantly designed into it. if you get stop paying us youll get sick and even better withdraw. and the whole time its becoming less and less effective as your body gets used to it but the toxins and waste and chemicals build up in your body to new heights. there's no money in the cure. so lets all dump chemicals into ourselves indefinately with "side" effects worse than the disease it "cures" just long enough to become addicted to it. you have allergy meds with "side" effects bad enough to make you stay inside where the allergins aren't. you have depression meds with "side" effects of anxiety, depression and suicide. you have toxic interactions between all these things if youre taking more than one. and theyre laughing all the way to the bank. i bet you the people that own and run the pharma companies and the scientists dont touch that crap. who's to blame? who's not to blame. obviously the pharma industry, but what about you? the sheeple hypnotized by the flickering box who accept the construct of the world the way its handed to you by those holding clear interest in your reaction to it - thats called a conflict of interest. how about the govt? these companies are allowed to do everything short of write the doc a check and its legal. expensive dinners, hundreds of dollars in office supplies that they dont have to spend, vacations. what about the docs who accecpt all that? if you go into an office whatever drug name is plastered all over there crap is what youre gonna get. the newest, untried thing that company is pushing when something safer and cheaper thats been around for years will do fine with less "side" effects. a few months ago a landmark case at the supreme court. a woman lost her arm, sued the drug company, they said the warning was on the label so its not their problem. that doesnt sound evil? well she won the case. its a VERY important precident. how about all those poor bastards that died of heart attacks because the drug company falsified the tests to get it through the fda faster. you people are living in a different world than i am. and the day you instute projects for existing compounds used by drug companies or ones they want to test (unless its on your own to show how dangerous they are) i and my 1,860,000 points a year (based on aprils 90,500) team (until a couple months from now when i FINALLY move and break out my other 2 processors that have been in storage, thatll kick it over 2milli, and soon some us of are going to be investing in GPU - 3mi? 4mi?) are packing up and shutting down and saving our painful electric bills

[7im]

Whoa, dude. Grow some of your own medicine and chill out.