Modified Amino Acid Side Chain
Submitted by jferrie on Fri, 2016-06-17 08:13
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Loop design with length variation
Submitted by jarod on Thu, 2016-06-16 19:54
Category:
Design
Loop Modeling
hi all,
I am working on protein design for antibody-antigen complex to improve the binding affinity. so far, I have the crystal structure of the antigen (chain A) and the antibody Fab (chain H and L). now I want to re-design part region of one CDR loop (around 5 residues) involved in direct interaction to antigen. besides the design for the loop retaining original length (5 AA), I also try to make the loop shorter or longer with the randomizing the residues of loop.
any suggestion that where I can start from?
many thanks,
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Enumeration of Amino Acid identities
Submitted by achambe on Wed, 2016-06-15 15:28
Error while loading shared libraries: libcifparse.so
Submitted by mwid on Wed, 2016-06-15 12:08
Category:
Compilation
Hello,
I am trying to install CSRosetta and Rosetta on a computer running Fedora 20, but I keep on getting the following error message:
/home/crowlab/Rosetta/main/source/bin/AbinitioRelax.linuxgccrelease: error while loading shared libraries: libcifparse.so: cannot open shared object file: No such file or directory
We have CBFlib-0.9.5.1-1.fc20 package installed, but the software seems to not recognize it. We are not sure what we should have installed instead.
Thank you in advance for your help.
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Score Differences between Ab Initio Scoring and Rescore
Submitted by mmarlett on Wed, 2016-06-15 09:14
Category:
Structure prediction
I have a question about how atom coordinates are determined for predicted structures during the ab inito folding protocol and with the extraction of the PDB of the predicted structure from the output silent file.
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supercharge problems
Submitted by hooria on Tue, 2016-06-14 05:29
Category:
ROSIE
Dear Professor Bryan Der,
Thank you very much for your great server. I've come across two essential questions using your techniques and I really need your help so I can continue working on my PhD thesis.
I've used both supercharge methods:
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Unit Tests failing for Rosetta installed with mpi on Ubuntu 16.04
Submitted by abhi_pe_acharya on Mon, 2016-06-13 22:11
Category:
Compilation
Dear Users,
I have been trying to install and run Rosetta 2016.15 weekly build (with MPI) on a core i7 system on Ubuntu 16.04. For installation, I used the following command
> python ./scons.py mode=release extras=mpi bin
and compiled the test scripts using:
> python ./scons.py mode=release extras=mpi cat=test
The system already has openmpi-1.10.2. The installation was without any errors. However, when I ran the unit tests, I got numerous errors with a 27% pass statistic.
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Rosetta: Clustering
Submitted by sskim on Sat, 2016-06-11 14:44
Category:
Compilation
Hi,
I have used rosetta protein-protein docking to generate 1000 models, and was hoping to use rosetta clustering to analyze the result.
I have read that rosetta clustering superimposes models for rmsd calculation by default, and I was hoping to find a way to change this default mode for my models.
Is there a way to turn this default mode off?
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How to set up external C++ folding server
Submitted by seanle24245 on Sat, 2016-06-11 10:54
Category:
Structure prediction
For many of the Rosetta applications, I am required to connect to an external server to process my requests and handle the modeling and structure predictions. How exactly am I supposed to do this? Is there a detailed tutorial on how to do this? Or is it because I did not install PyRosetta correctly? I am doing comparatve modeling/structure prediction.
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Lammps or RosettaSurface
Submitted by StevPChem on Fri, 2016-06-10 10:13
Category:
Docking
Hello
I hope I placed this question in the proper place. If not please let me know.
I am attempting to computationally dock peptides/proteins to metal oxides etc..What is the most approbriate code to use RossettaSurface or Lammps? At the moment, I have installed PyRosetta and Lammps. Since there is a learning curve using these codes, I would like to select the best one to meet my needs. With LAMMPS, I believe there is versatility (i.e. alter atom types etc..); but I don't know about RosettaSurface..
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