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Thread: 99.989998 as best structure?

  1. 08-15-2002, 05:56 AM #1
    jlandgr
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    99.989998 as best structure?

    Hi,
    I can see that quite a number of people on our team who have already uploaded some work, like myself, have best structures of 99.989998.
    Is it a coincidence? Are better structures so hard to find for the current protein? Or is that a glitch?
    Appreciating any insights,
    Jerome
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  2. 08-15-2002, 06:28 AM #2
    tpdooley
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    The last protein ended with a best score of 41? and we're already down to a 45 as the current best score with this protein. (as of 3:21am PST). So I'd think that finding better scores is easier on this protein.
    The top 22 folks in the group I'm in are already down to 53-67 (except for one fellow that hasn't uploaded any data) - and we didn't get low scores like this on the last protein for days. (If I remember correctly).
    So just give it a bit more time and you should start finding some low scores, too.
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  3. 08-15-2002, 06:48 AM #3
    jlandgr
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    Well, it makes sense I assume if only score lower than 100 get displayed and if you, by bad luck, only got a score of 130 or so as your best score yet, then 99.989998 gets displayed. Or the function in the software in itself has a threshold and uses this value.
    I knew that my scores increased, I was just curious if that was some kind of glitch as several people had exactly this same value.
    But it probably is indeed only some thresholding and bad luck on our part thus far.
    Thanks,
    Jerome
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  4. 08-15-2002, 07:36 AM #4
    KWSN Grim Reaper
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    If you are dumping the old protein, your energy isn't going to change. I just dumped 600k and it still appears as though I am inactive because they were shrubs I couldn't upload last night.

    Ni!
    Oh, what sad times are these when passing ruffians can say Ni at will to old ladies..
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  5. 08-15-2002, 07:50 AM #5
    jlandgr
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    If you are dumping the old protein, your energy isn't going to change.
    Nope, but thanks, it's the new protein all right. AFAIK those who haven't uploaded any new proteins yet have 99.999901 which slightly differs from 99.989998 ;-)
    Jerome
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  6. 08-15-2002, 08:59 AM #6
    Brian the Fist
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    Ive already answered this before, but dont have time to look for that now. Basically, 99.0001 means nothing uploaded, 99.9899 means something uploaded but nothing compact enough to keep for further analysis - structures < 99.9899 were compact and more detailed energy scoring was calculated on them to get a value from 0 - 99 which varies from protein to protein.

    Similarly, this protein is slower because the speed is not only dependent on the length of the protein but on the makeup of it, some get stuck more than others, etc.
    Howard Feldman
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  7. 08-15-2002, 10:17 AM #7
    jlandgr
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    OK, thanks.
    Jerome
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  8. 08-15-2002, 07:29 PM #8
    GOLDENBALLSAINTYORK
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    protein structure delinration values

    Hi Folks!
    I have noticed with previous CASP candidates that certain values are returned with the same RMSD..Obviously the same protein has been folded to give the same energy level to err..4 dec. places...
    I'm sure that any evaluation of a particular structure..given only the amino acid residues will per se give a statistical eval. of that particular protein candidate...
    Not sure if I'm right here, but you'll see a shifted 'poisson distribution curve, which can be extrapolated with the number of structures 'crunched'...The length of the constructed AA's ie residues does not relate directly to 3D conforming of a particular structure, maybe due to the type of Amino acid residues to conform..
    A Sulphur atom or a Nitrogen atom in a res. I think might speed up processing, but with Carbon . Hydrogen etc?

    Also isomerisation might play a part..optical dl or dr?

    Takes me back to 1977 when we had to look a x-Ray diff on the old Vax VMS at Reading University..!!

    This is a shit hot project, I've been out of Science too long!
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    Keep folding!

    GOLDENBALLSAINTYORK
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  9. 08-15-2002, 07:40 PM #9
    GOLDENBALLSAINTYORK
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    As a p.s. Energy eval can only work within the confines of the biological environment it has to operate in ..the pH of the 'in vivo' structure and the other molecular parameters that interact with it..
    ATEOD we are looking at a statistical evaluation exercise
    Now where's my Sodium Dimethyl Glyoxime gone?
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