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Is there a way to make `modeller.addHydrogens` reproducible?
I am trying to calculate hydrogen bonds using MDTraj. In order to do that, I need a protonated PDB structure. I tried using OpenMM to a…
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On a clean `vaxrank` install:
```
vaxrank \
--vcf test/data/b16.f10/b16.vcf \
--bam test/data/b16.f10/b16.combined.bam \
--vaccine-peptide-length 25 \
--mhc-predictor netmhccons \
…
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Haven't debugged this, not sure what's really going on, but posting it here in case others see it:
```
---------------------------------------------------------------------------
OverflowError …
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http://doi.org/10.1101/078659
Related to #22. @cgreene can tell us more.
> Abundant public expression data capture gene expression across diverse conditions. These steady state mRNA measurements co…
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Hey guys, Alex asked me to run the mouse tumors through topiary to generated MHC-II predictions, but I'm having some difficulty running topiary w/ these settings. I've tried a bunch of different input…
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Hello,
We were looking for a MF terms to use for as peptide synthase. Our ferrichrome synthase currently has
ligase activity, forming carbon-nitrogen bonds
which did not seem specific enough.
This…
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Several small proteins such as UB, SUMO, and Rub/NEDD need to proteolytically processed before they can be attached to a target.
This requires the cleavage of a peptide bond within UB, SUMO, etc. (p…
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Line 156 in HRM Branch design_primers.py
```
mutamp_seq[target_feat.location.start]=target_feat.qualifiers['Variant_seq'][0] #mutate to variant
```
This fails with index states and needs to be made …
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We need to come to some consensus on basic features of the Turing test paper. I have tried to spell it out here in the issue. I have marked with first initial where I think some of you fall, but ple…