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World Community Grid Forums
Category: Completed Research
Forum: Human Proteome Folding - Phase 2
Thread: HPF2 Structure Comparison |
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Thread Status: Active Total posts in this thread: 5
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
As I understand it, both Genome Comparison and BOINC-SIMAP compare proteins based upon sequences.
----------------------------------------HPF2's goal is to provide structural data for all sequenced proteins, because structure provides more data. Once a sufficient repository of data for HPF2 is acquired (or HPF2 is finished), will there be a structure-structure comparitive analysis for predicted -> predicted/known protein structures? Is this a computationally intensive task that would require a new DC project? [Edit 1 times, last edit by Former Member at Feb 2, 2007 6:29:02 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi esoteric17,
Genome Comparison and SIMAP are comparing proteins using the 1-dimensional sequence to compute similarity. HPF2 is predicting the 3-dimensional structure. There are methods for computing the 'similarity' of 3-D structures, but this gets complicated. A similar 'exterior' is much more important biologically than the interior. I have not heard of anyone wanting to do a massive grand comparison. I suspect that a more targeted investigation will be the usual rule. Lawrence |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Hi esoteric17, Genome Comparison and SIMAP are comparing proteins using the 1-dimensional sequence to compute similarity. HPF2 is predicting the 3-dimensional structure. .... Lawrence Let's see if my car (automotive) analogy is correct? Protein structures are like a car. They all have four wheels, bodies, and doors. The 1-dimensional similarity is like letting the driver thru the door opening (nothing more) but the 3-dimensional comparison is also watching or letting the driver push the gas pedal and shift the thing, after getting inside? Lawrence, am I fairly correct here? |
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Brecht Crombez
Cruncher Joined: Oct 16, 2006 Post Count: 40 Status: Offline |
1D means that they compare the sequences of AminoAcids in different proteins
(a protein is a chain of AminoAcids) 3D means that they (also) compare the 'folding' of those AminoAcids-chains (the chain of AminoAcids is fold into an unique way for each protein, so this is the 3D structure of a protein) hopefully this is a clear explanation... greets |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
You have it right, Brecht Crombez!
For most folded proteins, what matters most biologically is the exterior boundary of atoms that it presents to the world for chemical interactions. A change in the interior sequence is important only if it moves the exterior around into a new shape. Lawrence |
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