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De novo structure building with medium resolution map

Category: 
Structure prediction

Dear all,

I am trying to build a model for my protein and I have a medium resolution map (~5-6 A). I tried backbone tracing manually, but many regions are dubious. This protein does not have any homologous protein either, so I am looking for tools to do denovo model building with guided electron density. Is there any available protocol to achieve this?

Best,

Buddy

Post Situation: 

Some erros while build denovo_density.cc

Category: 
Structure prediction

Hi,I have two question

1)How could i generate denovo_density.linuxgccrelease by source code?  Now I am trying to use denovo_density.cc to do this thing ,but i do not know if it is work?

2)While i use denovo_density.cc and many include files to rebulid the project whit clion ,i got this problem as follow:

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kcenters_clustering_of_fragments

Category: 
Fragment Generation

Hello Rosetta community,

I'm having trouble finding the fragment generation application "kcenters_clustering_of_fragments." The application is mentioned as publically available in the methods section of D.A. Silva et al (2019). De novo design of potent and selective mimics of IL-2 and IL-15. Nature. Link: https://www.nature.com/articles/s41586-018-0830-7?WT.feed_name=subjects_computational-biology-and-bioinformatics

Post Situation: 

Rosetta_cm Partial Threading Removing Parts of Sequence

Category: 
Structure prediction

Hello,

I am currently trying to homology model the PAR1 receptor with the P2Y12 receptor as my template structure, but for some reason I believe that parts of my sequence are being altered/removed, namely the loop regions.

For example, the original PAR1 sequence is as follows:

Post Situation: 

Mutations are ignored (fixbb) when using -auto_setup_metals option

Category: 
Design

When using fixbb.static.linuxgccrelease (2018 or 2019 release) with the -auto_setup_metals option set, see cmd line below, all mutations to a residue with a link to a metal ion, are ignored in the model generated (PDB file).

Run process: /usr/local/rosetta/main/source/bin/fixbb.static.linuxgccrelease -s ../src_updated_0001.pdb -extra_res_fa ../sub.params -resfile resfile-S100.txt -nstruct 1 -ex1 -ex2 -database /usr/local/rosetta/main/database -jran 1001 -constrain_relax_to_start_coords -use_input_sc -minimize_sidechains -overwrite -auto_setup_metals

Post Situation: 

VH-VL Orientation in antibody

Category: 
Structure prediction

 

How to determine the VH-VL orientation angle in rosetta. i came across this manuscript "Improved prediction of antibody VL–VH orientation" by Protein Eng Des Sel. 2016 Oct; 29(10): 409–418. Here there is description of MT protocol. Whether the script is provided in the rosetta 3.1 version. Or is there any other alternative in rosetta to calculate the VH-VL orientation (LHOC) angle of antibody in rosetta.

Post Situation: 

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