WeFold_CASP11

Structure Prediction Pipeline – Amber edition

Posted by in WeFold2

Hello, The focus of my work this past quarter has been in developing a pipeline that takes as input a prediction file (*.pred), and then outputs a selection of protein structure predictions (*.pdb) for that prediction file. Note : The following describes the Pipeline as it is on 6/4/14. The first stage in this process is a C++ parallel script, written almost entirely by a previous collaborator with professors Max and Crivelli, available in the resources, titled MPI.cpp (MPI being the name of the library the author chose to use for…read more

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Current Progress

Posted by in WeFold2

Hi, I have been working with Amber 12 during the quarter. We have been figuring out how to use it in order to do what we wanted. After fiddling around a bit with the program, I have created some scripts based on what I have working so far. Currently I run a PDB file generated by modeler which will help with the coil regions of the protein. Then, I run that through an amber nab program that will re-add the hydrogens into the structure as well as minimize the energy…read more

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Invitation is open

Posted by in WeFold2

WeFolders have generated 11 hybrid pipelines so far. Would you like to participate? Please join us! We contribute We collaborate We learn WeFold!

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CASP11 is here!

Posted by in WeFold2

CASP11 is finally here and we’re working on some very exciting pipelines. I’m going to post what we have so far in my next blog. Please feel free to propose pipelines that you’d like to try either using this forum or via email. There are 2 ways to upload files: If you want to upload a file, then click on the avatar next to your user name on the top right corner and then select “BuddyDrive”. Click on the first icon to the right of “Files” (a file with a…read more

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