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# Description
If we want to load PDB files with no connectivity data (such as those coming from PELE simulations) we need a method to assign the missing connectivity.
# Solution
We can use an `RD…
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This thread is for brainstorming ways in which we can find synergies between OpenMM and the Open Force Field Initiative.
cc: @j-wags @davidlmobley @andrrizzi @simonboothroyd
The [Open Force Fiel…
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Dear APBS community,
I would like to know if APBS can be used with coarse-grained protein structures (for example protein models with one pseudo-atom per residue) for which I know the relevant quan…
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There are 16 annotations from
Proteomics of the response of Arabidopsis thaliana to infection with Alternaria brassicicola.
Abstract
We have studied the proteome of the model plant Arabidopsis …
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### Background
Based on implementing option 2: https://github.com/AlexsLemonade/refinebio-examples/issues/340#issuecomment-723272256, we need to draft up a paragraph with the essential info of how …
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Dear developers, I have tried to take a look at the example given, with a freshly installed VMD version and sadly it just crashed the program. I am not sure if this is an issue with VMD itself, or the…
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I used "trinotate_report_summary.pl" of Trinotate (https://github.com/Trinotate/Trinotate/releases/tag/Trinotate-v3.2.1) to generate a "cXp_summary.html" file, however, this html file shows up blank w…
ljyls updated
4 years ago
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About the interaction between molecules
Description
I want to know if I can do intermolecular interaction through this plugin.?
Relevant Context
I want to click on a certain molecular structur…
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### Background
Per [this related comment on PR #347](https://github.com/AlexsLemonade/refinebio-examples/pull/347#pullrequestreview-530420731), the microarray pathway analysis GSVA example notebook…
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I'm opening this as a place to describe something I'm working on and get feedback about it.
We recently changed the molnet loader functions to use scaffold splitting instead of random splitting, wh…