The hbond for REF2015
Submitted by asbelx on Mon, 2022-06-06 06:07
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Scoring
ShapeSimilarity, ElectrostaticSimilarity (RosettaSurf)
Submitted by Ken on Mon, 2022-05-23 07:16
Category:
Scoring
Hi all,
I would like to try out ShapeSimilarity and ElectrostaticSimilarity filters that were described in the 3.13 release notes (https://www.rosettacommons.org/docs/latest/release-notes), but the links on that page says it's "Forbidden. This Wiki is set to no-edit mode." I tried adding it to Rosetta script and I get "This element is not expected" error. Would somebody be able to point me to the right direction?
Best,
Ken
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Relax evaluates protein-DNA complexes?
Submitted by pablogalazdavison on Thu, 2022-05-12 12:05
Category:
Scoring
Dear users,
I'm currently working on generating a DNA complexed protein and I thought I could use the relax application to avoid steric clashes generated during the "copy/paste" approach I used to put the DNA and protein together (after alignment with previously solved structure).
Does anybody have experience with improving the quality of DNA-protein complexes through Rosetta? my aim is to prepare the PDB for conventional molecular dynamics.
Any help is appreciated.
Pablo
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InterfaceDdGMover and ResfileReader
Submitted by asaf.farhi on Wed, 2022-04-13 15:05
Category:
Scoring
Dear all,
I have two issues with Rosetta and I would really appreciate your help.
The first one is in InterfaceDdGMover
"In InterfaceDdGMover, there are no valid chains to translate when unbinding!"
The second one on another system is in ResfileReader:
"On line 3, the pose does not have residue with chain=B, PDBnum=417."
Thank you very much,
Best regards,
Asaf
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Weekly releases for commercial users?
Submitted by rjacak on Tue, 2022-03-22 07:48
Category:
Compilation
Structure prediction
Docking
Design
Scoring
Enzyme Design
Loop Modeling
Constraints
Symmetry
Small Molecules
Chemically Modified Residues
Fragment Generation
Hi Steven, Rocco, et al.,
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Differentiable Energy Function w/ Centroid Representation
Submitted by protein_fan on Sun, 2022-03-20 09:39
Category:
Scoring
Hi!
I have a protein complex that's represented in terms of the sequence, the pairwise distances between the CA atoms, and the phi and psi dihedral angles. These distances and dihedral angles should be reasonably correct. I do not have access to the coordinates (N,CA,C,O, etc.) of this protein complex.
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Modelling at defined pH - for pmutscan - pH:mode not working
Submitted by cagfa1 on Tue, 2022-03-15 04:05
Category:
Scoring
Loop Modeling
Chemically Modified Residues
Hi all,
I am new to Rosetta and using various Rosetta protocols, primarily remodel and pmutscan, to assess the impact of various mutations on protein stability. I would like to model the protein and associated mutations at acidic pH as this may affect salt bridge formation and overall REU score.
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Inconsistent scoring by "aa_composition" term
Submitted by chenna on Thu, 2022-02-24 03:00
Category:
Scoring
Dear Community,
I have noticed an inconsistency in the scoring of a designed sequence on using the "aa_composition" term.
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I_sc
Submitted by Soler on Sat, 2022-02-12 00:16
Category:
Scoring
Hello, I would like to use or be able to visualize in the score file some terms or information related to docking and similar protocols, for example, interface_score and rms in other scoring functions executing other movers. Can this be done with flags? I hope you can help me, thanks.
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Acessing energies terms from energy.show() table
Submitted by João Sartori on Mon, 2022-02-07 07:56
Category:
Scoring
I am trying to get the individual values from each energy term from my pose to save in a dataframe, but i still haven't find i way to do this, there is a simple way to do this?
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