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Category: Completed Research
Forum: Microbiome Immunity Project
Thread: What exactly does one crunch for a task? |
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Thread Status: Active Total posts in this thread: 7
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hello,
----------------------------------------I'm relatively new here and received Ruby Badge yesterday from Microbiome Immunity Project. I support the project because a good friend has an illness where the research can be improved by crunching tasks. I'd like to better understand what you crunch exactly and how it fits into the big picture. The screen of a task says: "predicting structure of a protein coded by a bacteria's gene" I do not know my way around the area. There are bacteria whose genes consist of proteins. And these proteins are crunched, right? How many genes does a bacterium have and how many bacteria are there? In short, I would like to know what impact the crunching of a task has. Can someone explain this in more detail or is there clear information about it? Thanks in advance! And please excuse me if I did not express myself well. English is not my mother tongue. [Edit 1 times, last edit by Former Member at Jul 31, 2018 12:25:37 PM] |
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BladeD
Ace Cruncher USA Joined: Nov 17, 2004 Post Count: 28976 Status: Offline Project Badges: 
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Start here .
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Jim1348
Veteran Cruncher USA Joined: Jul 13, 2009 Post Count: 1066 Status: Offline Project Badges: 
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That raises an interesting question. Since MIP makes use of the Rosetta app, is it really a protein folding project?
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Sgt.Joe
Ace Cruncher USA Joined: Jul 4, 2006 Post Count: 7846 Status: Offline Project Badges: 
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That raises an interesting question. Since MIP makes use of the Rosetta app, is it really a protein folding project? In a sense you are right, but I think it is more complicated than just that. First they (the scientists) need to identify the various bacteria types which comprise the human biome. Then they need to figure out the genetic code for all those different types of bacteria. Then they need to figure out what proteins are coded by that bacterial genome. Once the proteins are identified, then the structure of the protein needs to be determined. As part of this determination of the structure is how the protein itself is folded. Even though two identical protein structures are the same, the way they fold, for instance, either in a right hand manner or a left hand manner, can alter the manner in which they function. Please correct me if I am off base here. Cheers
Sgt. Joe
*Minnesota Crunchers* |
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Jim1348
Veteran Cruncher USA Joined: Jul 13, 2009 Post Count: 1066 Status: Offline Project Badges:
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Thanks. That is quite good enough. I figured it included something else, or it would just be Rosetta.
By the way, Rosetta also suffers from the problem of reduced output when you run too many at once. I limit MIP to two at at time, and Rosetta to five or six at a time on my eight-core CPUs. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
That raises an interesting question. Since MIP makes use of the Rosetta app, is it really a protein folding project? In a sense you are right, but I think it is more complicated than just that. First they (the scientists) need to identify the various bacteria types which comprise the human biome. Then they need to figure out the genetic code for all those different types of bacteria. Then they need to figure out what proteins are coded by that bacterial genome. Once the proteins are identified, then the structure of the protein needs to be determined. As part of this determination of the structure is how the protein itself is folded. Even though two identical protein structures are the same, the way they fold, for instance, either in a right hand manner or a left hand manner, can alter the manner in which they function. Please correct me if I am off base here. Cheers Thanks, your explanation make things much clearer for me! I understand that there are about 3 million bacteria forming Human's Microbiome. Can be estimated how many proteins there are which are coded by that bacterial genome? The number of proteins should then also correspond to the approximate amount of tasks, shouldn't it? |
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KerSamson
Master Cruncher Switzerland Joined: Jan 29, 2007 Post Count: 1684 Status: Offline Project Badges:
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Some sizing figures regarding the human microbiota (microbiome):
----------------------------------------- Estimated (+/-25%) average number of microorganisms: 39 trillions (3.9 x 10 exp 13) - 1 kg microorganisms in the microbiota for a 70-kg man) - Complexity of the metagenome: 3.3 millions genes (vs 22'500 genes for the human genome) (sources https://fr.wikipedia.org/wiki/Microbiote_intestinal_humain, https://en.wikipedia.org/wiki/Human_microbiota) Cheers, Yves ---------------------------------------- [Edit 1 times, last edit by KerSamson at Aug 1, 2018 10:52:59 PM] |
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