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From a usability perspective, I would suggest that sequences with unsupported amino acids be skipped and warnings be issued. The current behavior simply has the program crash with a KeyError. The note…
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I used conditional sequence generation via evodiff.ipynb with my own MSA file.
However it came with a amino acid sequence containing un-natural amino acid codes such as "Z" and "B"
And i would lik…
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How were the probabilities for amino acids in the class `BaseSequence()` calculated? Particularly, how was `prob_ACPhel `computed?
Thank You!
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SPICE 2 is close to finished, which means this is a good time to discuss possible additions for version 3. Here are some ideas to get things started.
- **Nonbonded interactions between amino acids…
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Character color coding schema for 21 character of the amino acids. Get further information from the professors
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Martini22 legend
Amino acids side chains ?
Structural information ?
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The current (prototype) implementation of the package does not include any energy-using mechanisms. At a minimum, we should create versions of transcription and translation that use up NTPs and amino…
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Hello.
This is related to #44
I am exploring if there is a possibility to add hundreds of non-canonical amino acids to templates and soft.xml to allow for mutating standard residues to any of the…
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could you upload the biophysical features for 20 standard amino acids?