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Dear Author,
Thank you for developing such a perfect model like C.Origami. It's a great work, but I have encountered some difficulties.
First, I have DNA sequence information from other species,…
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Awhile ago I made a biopython issue mentioning a small bug I saw in the DNA nearest neighbor values. I caught that because I was using biopython's DNA nearest neighbor energies to bootstrap a library …
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Your recent article(Nat. Mat, 2024) proposes a method for predicting DNA origami structure using graph neural networks. I think it's very powerful and exciting. I want to know how to use the function …
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I am trying to model a protein homodimer complexed with dsDNA. I have entered in the two identical protein monomer chains as separate files and DNA strands as two separate files. In a command similar …
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Hi,
AptaSuite asks for using CapR for secondary structures prediction but this program calculates RNA folding. Do you have any suggestions how to involve DNA secondary structure prediction in AptaSu…
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Amino acid sequence module. Show protease cut markers. Show automated annotation, including secondary structure prediction, Chou-Fasman, coiled-coil prediction, etc. Allow backtranslation into DNA, ba…
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request from @bebatut
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Hello Developers,
I’m trying to use `mxfold2` to predict for some RNA sequences. However, I encountered a inconsistent result between my local prediction and the web service at `http://www.dna.bi…
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I worked a bit on the labelling matching with ENA / NCBI as I had a lot of mismatch issues with the development of the FAIR Data Station. I forked the repo and did an analysis on the terms in MIxS and…
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- [ ] Datasets
- [ ] AlphaFold 3 PDB dataset
- [x] PDB mmCIF filtering script (`scripts/filter_pdb_mmcifs.py`)
- [x] Fix periodic residue count-chemical component coun…