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Hello. Thank you for making this great tool open-source. Is support for other types of molecules besides proteins on the roadmap for FoldSeek's development?
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In the file: *zGetNTData*, the warning **has overlapping nucleotides and should be used with caution** is produced when the array `d`, the atom distances has the condition
if d(min(10, len…
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Here i am using below code for calculation of ermsd of RNA system by using gromacs trajectry file. And i got an error like Error...
Can anyone help me regarding this?
Thank you
`import barnaba …
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Potentially related to #158
I've been trying to parameterise a protein ( [bace_prep_nowats.pdb.tar.gz](https://github.com/michellab/BioSimSpace/files/5446929/bace_prep_nowats.pdb.tar.gz) ) without…
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1. As a next step for this project, Marc should try to retrain the MXfold2 PyTorch models to see if the retrained model can reproduce the performance using the same neural network architecture and par…
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I have tested e2efold on a set of 361 PDB chains, where secondary structures for RNAs shorter than 600 nucleotides are predicted by ``e2efold_productive/e2efold_productive_short.py``, while those lon…
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How can I get more information about exceptions presented below?
```
An exception of type 'System.IO.FileNotFoundException' occurred in MBrace.Core.dll but was not handled in user code
Additional in…
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I encountered a problem while reading file 488D.pdb. It enters infinite loop in file zBorderSS at line 121 and newer leaves. Used zAddNTData to read file.
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[1] As we discussed today, it is not correct to combine all three subsets of SPOT-RNA PDB dataset into one single set. Instead, you should train on the training set (TR1), validate hyperparameters (e.…
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A video tutorial on this process can be found here: https://www.youtube.com/watch?v=ZnXBa9RdliU
![Untitled video (2)](https://github.com/TomkUCL/SARS-CoV-2-Helicase-nsp13-Public-Antivirals-Virtual-…