Crossdocking

Message boards : Docking@Home Science : Crossdocking

Author	Message
Eduard Bentea Joined: Nov 1 09 Posts: 2 ID: 20996 Credit: 556,067 RAC: 0	Message 5751 - Posted 6 Mar 2010 21:48:57 UTC
	I was just wondering about a couple of things regarding these new crossdocking simulations. What exactly are you hoping to conclude from them? Are you trying to dock a ligand known to work (in a real-life, experimental set-up) to different conformations of the same protein in hope to get positive results through-out (and thus validate the molecular optimization algorithm)? Also are you testing to see if a ligand which is known not to work, will actually bind in silico for a certain protein configuration (and thus detect false positives, and reject the algorithm). I noticed different work units with the same protein-ligand complex, and I assume that you are following the first route, but I was just curious. Also, in these mod0013b work units, are you also simulating the solvent? In any case, I just want to say that I really like how D@H is evolving, congratulations and keep up the good work! If you manage to validate this algorithm by considering the flexibility of the protein, I guess it would be quite a feat.
	ID: 5751 \| Rating: 0 \| rate: /

Trilce Estrada Forum moderator Project administrator Project developer Project tester Joined: Sep 19 06 Posts: 189 ID: 119 Credit: 1,217,236 RAC: 0	Message 5903 - Posted 7 Apr 2010 20:15:04 UTC
	Hi Eduard, Thank you for your note, and I'm sorry I didn't respond before, as you might have seen after march 7 we had a crisis here. Fortunately everything is better now, and I had time to check the other threads of the forums. Yes, we are indeed following the first route you mentioned. I'm sure that in the future, when our algorithms are strong we will follow also the second route and produce in that case more interesting results. Well, thank you again, this kind of comments make my day =) Best
	ID: 5903 \| Rating: 0 \| rate: /

Message boards : Docking@Home Science : Crossdocking

Database Error
: The MySQL server is running with the --read-only option so it cannot execute this statement

array(3) {
  [0]=>
  array(7) {
    ["file"]=>
    string(47) "/boinc/projects/docking/html_v2/inc/db_conn.inc"
    ["line"]=>
    int(97)
    ["function"]=>
    string(8) "do_query"
    ["class"]=>
    string(6) "DbConn"
    ["object"]=>
    object(DbConn)#7 (2) {
      ["db_conn"]=>
      resource(60) of type (mysql link persistent)
      ["db_name"]=>
      string(7) "docking"
    }
    ["type"]=>
    string(2) "->"
    ["args"]=>
    array(1) {
      [0]=>
      &string(51) "update DBNAME.thread set views=views+1 where id=515"
    }
  }
  [1]=>
  array(7) {
    ["file"]=>
    string(48) "/boinc/projects/docking/html_v2/inc/forum_db.inc"
    ["line"]=>
    int(60)
    ["function"]=>
    string(6) "update"
    ["class"]=>
    string(6) "DbConn"
    ["object"]=>
    object(DbConn)#7 (2) {
      ["db_conn"]=>
      resource(60) of type (mysql link persistent)
      ["db_name"]=>
      string(7) "docking"
    }
    ["type"]=>
    string(2) "->"
    ["args"]=>
    array(3) {
      [0]=>
      object(BoincThread)#3 (16) {
        ["id"]=>
        string(3) "515"
        ["forum"]=>
        string(1) "1"
        ["owner"]=>
        string(5) "20996"
        ["status"]=>
        string(1) "0"
        ["title"]=>
        string(12) "Crossdocking"
        ["timestamp"]=>
        string(10) "1270671304"
        ["views"]=>
        string(3) "236"
        ["replies"]=>
        string(1) "1"
        ["activity"]=>
        string(19) "1.2827042427082e-75"
        ["sufferers"]=>
        string(1) "0"
        ["score"]=>
        string(1) "0"
        ["votes"]=>
        string(1) "0"
        ["create_time"]=>
        string(10) "1267912137"
        ["hidden"]=>
        string(1) "0"
        ["sticky"]=>
        string(1) "0"
        ["locked"]=>
        string(1) "0"
      }
      [1]=>
      &string(6) "thread"
      [2]=>
      &string(13) "views=views+1"
    }
  }
  [2]=>
  array(7) {
    ["file"]=>
    string(63) "/boinc/projects/docking/html_v2/user/community/forum/thread.php"
    ["line"]=>
    int(184)
    ["function"]=>
    string(6) "update"
    ["class"]=>
    string(11) "BoincThread"
    ["object"]=>
    object(BoincThread)#3 (16) {
      ["id"]=>
      string(3) "515"
      ["forum"]=>
      string(1) "1"
      ["owner"]=>
      string(5) "20996"
      ["status"]=>
      string(1) "0"
      ["title"]=>
      string(12) "Crossdocking"
      ["timestamp"]=>
      string(10) "1270671304"
      ["views"]=>
      string(3) "236"
      ["replies"]=>
      string(1) "1"
      ["activity"]=>
      string(19) "1.2827042427082e-75"
      ["sufferers"]=>
      string(1) "0"
      ["score"]=>
      string(1) "0"
      ["votes"]=>
      string(1) "0"
      ["create_time"]=>
      string(10) "1267912137"
      ["hidden"]=>
      string(1) "0"
      ["sticky"]=>
      string(1) "0"
      ["locked"]=>
      string(1) "0"
    }
    ["type"]=>
    string(2) "->"
    ["args"]=>
    array(1) {
      [0]=>
      &string(13) "views=views+1"
    }
  }
}

query: update docking.thread set views=views+1 where id=515