Hello everyone,
I have an 18 subunit, helical enzyme that I'm trying to make more stable. I have, however, truncated it to include only one of each interacting surface.
Dear Rosetta experts,
I have been using rosetta mainly for refinement and iterative local rebuilding into cryo-em densities at reolustions of ~3-3.5 Angstrom. I am wondering how (or if it is possible) to combine and complete a set of backbone fragments predicted by external software into a single backbone trace using rosetta. To make matters somewhat more complicated I would need to do this without any sequence information using only polyA fragments.
Hi, everyone!
Hello,
Can the BuriedUnsatHbonds2 filter be pushed to release? It gets called in a rosetta scripts xml included in the supplementary materials for this paper (published in 2017): DOI: 10.1126/science.aan0693
Thanks!
Hi All,
I am working on designing some symmetric structures and am currently using REF2015 + hbnet. In addition, I want to add the buried_unsatisfied_penalty. When I add this term to the score function, it works and can score 'non-symmetrized' structures just fine. However, when I try to score a structure that has been 'symmetrized' I get the following error:
File: /home/benchmark/rosetta/source/src/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.cc:637
[ ERROR ] UtilityExitException
I am trying to do antibody design with the RosettaAntibodyDesign, but some of my colleagues told me that they fell to obtain successful designers with the RosettaAntibodyDesign (RAbD). They ran the RosettaAntibodyDesign on the crystal structure of an ab-ag complex with a dG_seperate of about -20 REU, and got some designers with dG_seperate of about -40 REU. However, they did experiments including ELISA and SPR and found that these antibody designers did not bind to the antigen at all!
Dear all,
The MHC Epitope energy (mhc_epitope) alogrithm (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/MHCEpitopeEnergy) is for deimmunization of epitopes. However I cannot understand how to use it.
I used the pdb file 2b3p.pdb and the score controlling script in the introduction webpage as the inputs and run the following command:
Dear developers,
I tried to follow the antibody design protocol from the Nature protocol articles but unfortunately I keep getting the following error when I try it:
core.pose.util: [ ERROR ] Can't find residue type 'UNK' in type set of mode fa_standard
This is my command line:
antibody.default.linuxgccrelease -ignore_unrecognized_res -fasta antibody_chains.fasta
and this is the content of ROSETTA_CRASH.log:
Hello all, I am using the antibody.mpi.linuxgccrelease to model multiple antibodies. Most work fine but about 10% are failing with weird error messages. I have tried everything to figure out the problem but am having no luck. These antibodies are clinical molecules, and so I feel like my failure rate is pretty high, and I'm probably doing something wrong. There is not a lot of documentation about the (newer) antibody homology modelling application and so I am a little bit at a loss as what to do to make the program more robust. Thanks as usual for all your help!!!
Hello
Is it possible to use a protein single state design protocol to increase a protein's affinity towards a ligand? Any suggestions are appreciated.
