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When fetching interactions if any connection error occurs fetch process is ended. It might be good if there is a --max-try parameter to continue trying after this error.
Error message is below;
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Hi @zzhangzzhang ,
Great study! I'm interested in using the Categorical Jacobian method as a evaluation tool for protein LMs. Can you please provide this `data/exp_pdb_seq.json` file or how to gen…
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Hi! Is the PISA API working?
I currently have a series of unp_ids, such as ['Q5VTD9', 'Q6PL24', 'Q9UKM9', 'Q9H0A3', 'Q9P2N6', 'P21127', 'Q8TD94', 'Q86SH2', 'Q9BYR3', 'Q99856']. How can I retrieve fo…
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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB
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**Date**: Sep 10th 2024
**Time**: 2pm UK time [other timezones](https://www.timeanddate.com/worldclock/meetingdetails.html?year=2024&month=9&day=10&hour=13&min=0&sec=0&p1=43&p2=136&p3=37&p4=771&p5=23…
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Hello.
Thanks for this awesome work.
I have a protein-ligand system parameterized with openff. I can save it as amber format parm7 or prmtop files. But, it's not very straightforward to save frc…
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I went back and had a look at the [NGL viewer](https://opensourceantibiotics.github.io/murligase/ngl/examples/MurDwebapp.html?script=interactive/MurD_ligand-viewer) of Fragment 373 for MurD (#1) and n…
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[error.txt](https://github.com/luancarvalhomartins/PyAutoFEP/files/12738015/error.txt)
Sorry to trouble you again.When I tried to use the tutorial 01 manual method to deal with receptors other than 5…
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## 🐛 Bug
Standard featurizers like GraphConv and AtomicConvFeaturizer no longer featurize PDB Bind dataset loaded with `load_pdbbind()` or if they do, result in incompatible dataset datatypes with …
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Project: ENCODE
So - we are working with a new High Throughput Sequencing Assay: icSHAPE, that captures RNA secondary structure.
NTR: "icSHAPE"
Editor preferred term: "icSHAPE"
Alternative…