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Hi, I saw that the initial guess used AF2 pTM model rather than multimer model for prediction. I wonder have you tested the Multimer model plus initial position of designed complex for in silico vali…
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**Tasks:**
- Decide and acquire a domain with all members of PTM (?)
- Configure domain to work with github pages ([Example how-to documentation](https://www.namecheap.com/support/knowledgebase/arti…
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**Issue by [Potentiam](https://github.com/Potentiam)**
_Thursday Mar 15, 2018 at 11:33 GMT_
_Originally opened as https://github.com/forkdelta/tokenbase/issues/558_
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Contract address: 0x7c3…
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### What happened?
Hello
So i'm in a bit of a pickle atm. I'm currently running `1.36.1`, but there is a fix in `1.40.1` for something else i would like. I digress.
But all versions past `1.3…
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Throughout PSI-MOD, when a heavy labelled atom is added in place of a "regular" atom, it's listed as
(12)C -X (13)C X , where X is the number of atoms being replaced.
Technically this is wrong,…
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line 385 of gromacs/templates.py (vdwlamdas):
`couple-intramol = vdw-q` throws an error in gromacs v2024.3; it's either "yes" or "no" now.
change to `couple-intramol = yes` ?
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Hi,
I have the same error with this #1684. It seems like it was fixed. Please let me know what I should do to avoid this error.
```
java.lang.ArrayIndexOutOfBoundsException: Index 0 out of bounds f…
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Hello,
When using the Fragpipe, I have a problem with the modification setting. How to set a modification not C-term, like this in Spectronaut?
![Capture](https://github.com/user-attachments/asset…
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I think we should modify how Casanovo reports PTMs in its predicted sequences. Ideally, we would be compatible with the Proforma specification:
https://github.com/HUPO-PSI/ProForma/blob/master/Spe…
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Yesterdays protein modeling gave the following log output with regard to the ranking of the five generated models:
`2023-09-22 18:52:35,633 alphafold2_ptm_model_1_seed_000 recycle=0 pLDDT=88.1 pTM=…