Posts by natteruw
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Message boards :
Number crunching :
Minirosetta 3.59
(Message 78553)
Posted 7 Aug 2015 by natteruw Post: Hi P.P.L., Just to check, did your edit indicate that the errors were somehow resolved? I submitted those C3C3P2123xtal_ jobs and most of them seem to have worked... Looking forward to your response, natteruw Getting a lot of errors on these tasks. |
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Message boards :
Rosetta@home Science :
protein-protein docking at Rosetta@Home
(Message 78172)
Posted 30 Apr 2015 by natteruw Post: Hi Rosetta@home, I am a new graduate student in the Baker lab, also working on protein-protein docking. Most recently, I submitted some docking runs with the tag "UN_top154_hboligomer." My project is more focused on utilizing the docking tools created by previous lab members to validate designs of two-component protein symmetric oligomers. Think, for example, of a clover leaf, which has 3-fold symmetry. That would be an example of a C3 symmetric oligomer. By two-component, I mean that there is a base C3, for example, that has single proteins binding/docking to the outside and "growing" outwards from it. The docking runs will help me computationally validate designs to decide which ones to order. These designs will serve as building blocks for protein materials that could have applications in general research techniques, health, energy, and environment. For example, a recent publication from the lab (http://www.bakerlab.org/Accurate-design-of-co-assembling-multi-component-protein-nanomaterials/) highlights symmetric oligomers being used to design protein "nanocages," which could be used for drug delivery or for scaffolding biofuel production. Thank you very much for donating your computer time for these protocols. Despite not always being in touch with the Rosetta@home community, we do sincerely appreciate what you are doing. I will try my best to continue watching the forum. Please let me know if you have any questions about what I have said or other older projects that you are still curious about. Best, natteruw |
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Message boards :
Number crunching :
Minirosetta 3.54
(Message 78170)
Posted 28 Apr 2015 by natteruw Post: Protein biomaterials have a lot of potential applications in health, energy, environment, and maybe even electronics. Recently, for example, a paper was published on protein "nanocages" designed by members of the Rosetta group. These could be used for drug delivery or localizing enzymes for things like biofuel production. (http://www.bakerlab.org/Accurate-design-of-co-assembling-multi-component-protein-nanomaterials/) [quote] |
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Message boards :
Number crunching :
Minirosetta 3.54
(Message 78159)
Posted 24 Apr 2015 by natteruw Post: Hi all, I apologize for those of you who have experienced job crashes related to any of the follow jobs: R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0002 R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0003 R00027_dSASA1633.3_2layerC3SB13_Ttj04_NMdock_0013_0001_A_asu_0_0005 R01463_dSASA1439.3_5H2LD1_Ttj05_NMdock_0019_0001_C_asu_1_0001 R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0001 R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0002 R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0003 R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0004 R02027_dSASA1494.4_5L8HC46_Ttj04_NMdock_0005_0001_A_asu_0_0005 They have all been taken off of Rosetta@home. These jobs may have been different enough from ones that had been tested on a local computer that they should have been tested themselves beforehand. I will try my best such that this does not happen again. In case you are wondering what I am trying to computationally validate...I am designing symmetric oligomers, which are proteins that self-assemble into a symmetric complex (for example, a clover leaf has 3-fold symmetry). What is special about these oligomers is that they consist of two building blocks that we have already experimentally characterized that are now undergoing a designed fusion meaning that the two pieces will become one, and should self-assemble. I am trying to test their docking on Rosetta@home. These could be extremely useful as building blocks for making protein biomaterials. Let me know if you have any questions about the job crashes or the project :) Best, natteruw |
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