I have been wondering whether it is possible to read the name of the protein from the task name. Does anyone know?

There are no strict pattern or format for the task names. Some project team members put the protein name in the task name as an identifer, but others do not. For some blind prediction jobs, we don't even know the protein name beforehand. If you have interest in any specific WUs, you can always ask and we will be happy to provide more information.

I have been wondering whether it is possible to read the name of the protein from the task name. Does anyone know?

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Welcome to Rosetta!

Possible? Yes.

Easy? ...not so much :)

You will notice a thread on each of the three message boards called the Project Information and Help Index. It's a sticky so it's always on the top of the list... at least up amongst the other stickies. Within it there is a link to the active work units log. That will give you more information about the various types of names presently being crunched. And the project information index will give you more information on many of the other questions you will likely have.

In addition to the FAQ mentioned in the Index, there's also the Q&A thread. Hope you find it useful.

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Hi pfkcmk. Welcome to Rosetta.

If there is a set of 4 characters in the task name such as some I have now "2snm" you can go to a protein data bank and type it into the search box. I use the RCSB Protein Data Bank. It doesn't always work but if you have a number and 3 letters it's usually in the data bank.

Bill

Hi pfkcmk. Welcome to Rosetta.

If there is a set of 4 characters in the task name such as some I have now "2snm" you can go to a protein data bank and type it into the search box. I use the RCSB Protein Data Bank. It doesn't always work but if you have a number and 3 letters it's usually in the data bank.

Bill

Thanks for the welcome. And thanks for the replies.

The problem is that the task name is not composed of 4 characters:
FRA_t369_test_LARS_constraints_newfrags_barcode_enforced_hom002_1_S_00001_0000614_0.pdbIGNORE_THE_REST_1436_4105
FRA_t369_test_LARS_constraints_hom001_1_S_00001_0000793_0.pdbIGNORE_THE_REST_1435_4209
FRA_t369_test_LARS_constraints_hom001_1_S_00001_0002792_0.pdbIGNORE_THE_REST_1435_4410
FRA_t369_test_LARS_constraints_hom001_1_S_00001_0000614_0.pdbIGNORE_THE_REST_1435_4630
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0007480_0.pdbIGNORE_THE_REST_1439_3769
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0007539_0.pdbIGNORE_THE_REST_1439_4862
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0006335_0.pdbIGNORE_THE_REST_1439_4901
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0006586_0.pdbIGNORE_THE_REST_1439_4705
FRA_t369_test_LARS_constraints_newfrags_barcode_enforced_PositiveControl_hom004_1_S_00001_0005627_0.pdbIGNORE_THE_REST_1443_673

These make me wonder what each string stands for.

FRA: fullatom relax -- a high-resolution refinement step for Rosetta structure prediction protocol.

t369: the protein being test, which is the target 369 from the recent CASP competation. As CASP is a blind structure prediction experiment, the participants like us did not know the structure or its real name before hand. So t369 is used here. Although the competition was already over in this summer, we are testing more ideas on how to improve our prediction methodology.

rest: probably only understood by those who actually submitted the tasks:-)

Hi pfkcmk. Welcome to Rosetta.

If there is a set of 4 characters in the task name such as some I have now "2snm" you can go to a protein data bank and type it into the search box. I use the RCSB Protein Data Bank. It doesn't always work but if you have a number and 3 letters it's usually in the data bank.

Bill

Thanks for the welcome. And thanks for the replies.

The problem is that the task name is not composed of 4 characters:
FRA_t369_test_LARS_constraints_newfrags_barcode_enforced_hom002_1_S_00001_0000614_0.pdbIGNORE_THE_REST_1436_4105
FRA_t369_test_LARS_constraints_hom001_1_S_00001_0000793_0.pdbIGNORE_THE_REST_1435_4209
FRA_t369_test_LARS_constraints_hom001_1_S_00001_0002792_0.pdbIGNORE_THE_REST_1435_4410
FRA_t369_test_LARS_constraints_hom001_1_S_00001_0000614_0.pdbIGNORE_THE_REST_1435_4630
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0007480_0.pdbIGNORE_THE_REST_1439_3769
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0007539_0.pdbIGNORE_THE_REST_1439_4862
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0006335_0.pdbIGNORE_THE_REST_1439_4901
FRA_t369_test_LARS_constraints_hom001_2_S_00001_0006586_0.pdbIGNORE_THE_REST_1439_4705
FRA_t369_test_LARS_constraints_newfrags_barcode_enforced_PositiveControl_hom004_1_S_00001_0005627_0.pdbIGNORE_THE_REST_1443_673

These make me wonder what each string stands for.

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Now that CASP is completed, you can actually see what the t369 was experimentally shown to look like on the CASP website

The best prediction will be the lowest line on the graph, so from this chart, you can also see that the models Rosetta found (show as black lines) were very good, but not the best of those submitted. And that would be why the project team is studying this protein in more detail. Asking that nagging question "how could we have known the structure would have looked like that?" and "how could we have figured that out with less computing power?"

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Rosetta Moderator: Mod.Sense

I understand much more now. Thank you for all the replies.