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I have designed several proteins which I predict have interactions with another protein using the sequence based Conjoint Triad Method. I would like to know which ones structurally are predicted to dock and have interactions. I have Rosetta installed and have looked at the examples a little. Rosetta doesn't have much "how to" documentation on protein design and fitness selection. Could someone please walk me through the process line by line of taking a fasta with a series of proteins through rosetta's ab initio pdb generation and then how to and where to look for a fitness of each proteins interaction/docking? Also I read in "Design of Protein-Protein Interaction Specificity Using Computational Methods and Experimental Library Screening" page 91 that it was possible to generate specific protein combinations that map to a structure using Rosetta. How do you do that? thank you :)

Rosetta commons links to additional software add ins but omits the crucial Sparks-X. I found Sparks-X from at this webpage. And I found that the code for make_fragments.pl needs to have many changes made for it to run properly. Several files are listed in make_fragments.pl. Two files without links pdb_seqres.txt and entries.idx are found at RSCB, below.

The NCBI nr database requires about 100 gigs of free space to properly load and process. Anything less than that results in errors.

make_fragments.pl requires a single gene in a fasta file. multiple genes in the fasta file cause it it crash.

Psipred nolonger has a dat4 so this line needs in make_fragments needs to have the dat4 removed.

"$PSIPRED sstmp.mtx $PSIPRED_DATA/weights.dat $PSIPRED_DATA/weights.dat2 $PSIPRED_DATA/weights.dat3 $PSIPRED_DATA/weights.dat4 > psipred_ss",

My make_fragments does not always finish it sometimes gives an error

ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!

This error was caused by a ^M in the fasta file removed with vi.

I'm attempting to bypass the fragment picker with csrosetta toolkit from .csrosetta.org/

libstdc++6 32bit version must be used for talos+ I used a Ubuntu 32 bit machine to copy the /usr/lib/libstdc++.so.6 and uploaded it here. http://www.mediafire.com/?j0133qqwiilsuz1

cs-rosetta does not create fragments for unknown reason. I have emailed the creator and I have emailed rosetta commons support as well. For now I recomend the on-line server roberta.

There are examples of how to use prepacking and docking in rosetta_tests.

PPI can be designed by docking a protein to another protein then running sequence tolerance. Though the resfile doesn't seem to be able to limit the changes to certain nt at this point.

Sequence tolerance has an extra rotamer bug and fills up memory and the page file for certain proteins if the "ex" series flags are use. It also sometimes ignores the resfile so double check the initial scripts results before begining a multi-generational study.

Ab initio relax has a bug which prevents it from running twice in the same directory. Remove default.out to rerun the structure prediction.

Docking can be forced to one location by using a constraints file but the radomize and spin options must be turned off for it to work properly.

-constraints:cst_weight integer -constraints:cst_file cstfile

http://www.rosettacommons.org/manuals/archive/rosetta3.4_user_guide/de/d50/constraint_file.html

http://www.rcsb.org/pdb/static.do?p=general_information/about_pdb/summaries.html

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closed as too broad by Mad Scientist Mar 23 at 13:33

There are either too many possible answers, or good answers would be too long for this format. Please add details to narrow the answer set or to isolate an issue that can be answered in a few paragraphs.If this question can be reworded to fit the rules in the help center, please edit the question.

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as this question is more concerned with how to use Rosetta instead of the biological implications, please ask it at biostars.org . There you're also more likely to get help. –  Michael Kuhn Sep 5 '12 at 7:00
    
@MichaelKuhn Theres nothing wrong with being a methodist. :) All good biology papers have a methods section and most journals require it. Protein-engineering is by definition a process...a group of methods. Rosetta is considered the best method as far as I know at the moment. "This is a free, community driven Q&A for biology researchers, academics, and students." –  caseyr547 Sep 8 '12 at 1:07
    
See the FAQ: "Questions on interdisciplinary subjects like bioinformatics are also welcome, as long as they focus on the biological part of the subject." –  Michael Kuhn Sep 9 '12 at 18:38
    
@MichaelKuhn this falls under "questions about techniques in a biological or biochemical laboratory". Dr. Keating's labs results are being reproduced. –  caseyr547 Sep 9 '12 at 23:48
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still its been quite a few days and nobody has given an answer... maybe not a bad idea to cross post –  shigeta Sep 11 '12 at 16:25