IMP-users July 2012

imp-users@salilab.org

2 participants
2 discussions

looking for ab initio structure prediction examples
by Adhikari, Badri (MU-Student) 25 Jul '12

25 Jul '12

Hello all, I have installed IMP nightly build and I can run all the examples. I am actually looking for an example that does ab initio protein structure prediction. The example http://www.salilab.org/~drussel/unstructured/imp_doc/atom_examples.html#str… does generate pdb files but I came to know that, this example does not actually do the structure prediction. It gives just the extended chain structures. Do we have any examples in which we can feed a sequence and get some models (probably pdb files)? Otherwise, what examples do we need to refer in order to do that? Once I do that, I plan to add other spatial restrains one by one and observe the changes in prediction after that. Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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can generate structure from sequences. how to add contact information as restrain?
by Adhikari, Badri (MU-Student) 09 Jul '12

09 Jul '12

Hello imp users and experts, I am using edited version of http://www.salilab.org/~drussel/unstructured/imp_doc/atom_examples.html#str… to generate structures from amino-acid sequences. This example uses IMP.atom.CHARMMTopology. I would like to feed contact information as a restrain to guide the prediction process. 1. What should be the approach? Which classes/functions should be used? 2. Are there any such examples? Sincerely, Badri Adhikari CS Graduate Student, University of Missouri-Columbia, Columbia, Missouri BAP54(a)mail.missouri.edu<mailto:BAP54@mail.missouri.edu>

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IMP-users July 2012