Posts by Brian Kidd

1) Message boards : Number crunching : Problems with version 5.96 (Message 52306) Posted 7 Apr 2008 by Brian Kidd Post: Thanks for letting us know about the large stdout files that you're getting. I'm currently looking into this issue and it looks like the error is basically harmless. We'll correct the large stdout files on the next release.
2) Message boards : Number crunching : Rosetta Application Version Release Log (Message 48406) Posted 6 Nov 2007 by Brian Kidd Post: Rosetta@home has been updated to 5.81. This version adds a new feature that allows us to properly model disulfide bonds in proteins.
3) Message boards : Number crunching : Problems with Rosetta version 5.81 (Message 48405) Posted 6 Nov 2007 by Brian Kidd Post: Thanks Trey. The thread link now points to the correct location.
4) Message boards : Rosetta@home Science : Rosetta@home Active WorkUnit(s) Log (Message 32317) Posted 9 Dec 2006 by Brian Kidd Post: A new job was just submitted - BAK_1klf_FimH_loop_model. This protein is a bacterial adhesion protein called FimH. The protein resides on the tip of projections that pathogenic e. coli extrude from their cell wall to stick to glycoproteins on the surface of human cells. The neat feature of this protein is that its binding is regulated by force, and the bond lifetime actually increases as force increases, called a "catch bond". This catch-like behavior is counter intuitive and contrary to how most bonds function - most bonds decrease their lifetime if you yank on them with more force. Predicting the structures of both states, active and inactive, would have huge implications for treating bacterial infections and developing novel molecular force sensors. FimH is an allosteric protein and the structure of the unbound - "inactive" - conformation has been technically difficult to solve by experimental methods. However, we ought to be able to predict the inactive structure with the loop modeling and full-atom relax techniques that we've been adapting to look at allosteric proteins. In addition, some recent work by our collaborators has given us reason to believe that there will be a NMR structure in the not too distant future. This experimental data will be a great validation for the predicted structures that you all are solving with Rosetta@home. Thanks so much for your support in predicting this structure.
5) Message boards : Rosetta@home Science : Rosetta@home Active WorkUnit(s) Log (Message 32315) Posted 9 Dec 2006 by Brian Kidd Post: I recently submitted a job (BAK_1avs_TnC_loop_model) to predict the structural changes in an allosteric protein called Troponin C. This protein regulates muscle contraction and has important health consequences for cardiovascular disease. In the near future, I will be submitting more workunits related to predicting conformational changes in allosteric proteins. For each submission, I'll describe a little about the protein's function and it's relevance to medicine or technology. As for allosteric proteins, they are particularly interesting cases for structure prediction because their function is regulated by structural changes that take place far from the active site. As a consequence these proteins have multiple functional states and we are attempting to predict the structures associated with these states. Our basic approach is to exhaustively sample the conformational away from the starting structure and look for additional energy minima. Thanks for your help in this important problem.