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Currently BioIn detects only the ligands associated with the PDB structures. Although it does not apparently affect the protein processing, many structures have a number of oligosaccharide molecules a…
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Hi,
Thank you for proposing the very smart new metric OmegaC and developing csubst. I'm not sure whether I understand it correctly, OmegaC is calculated by gene. After running csubst, we can know w…
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With huge structures like HIV viral capsid (3j3q)
I tried with rope representation and there is a huge preformances loss. Also the final result seems much heavier to handle by the browser using (``…
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Hi,
I have realized when I search against my target database in parallel mode, foldseek freezes. Yet, when I run it in single-threaded mode, it has no problem. The issue only arises with my attache…
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Provide a list of protein 3D structures as part of the protein details. PDB files are provided by #1355 and #1354. They need to be filtered based on the criteria developed by @jeet-vora and @rajamazum…
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## Motivation
Pangenomes are key to understanding the distribution of gene content and synteny across closely related genomes. Currently, the driving force behind this strategy is sequence alignmen…
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Hi all
I'm interested in generating contact maps from the ESM2 attention heads as described in the following github notebook:
https://github.com/facebookresearch/esm/blob/main/examples/contact_predi…
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http://www.wwpdb.org/download/downloads
> Since 1971, the Protein Data Bank archive (PDB) has served as the single repository of information about the 3D structures of proteins, nucleic acids, and co…
ghost updated
8 years ago
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thank you for your work, i want to replicate the model presented in this paper and apply it to my own research.
but i can not found the preprocess of inputdata, and where the 'datad_train', 'datad_va…
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Hi!
For my master thesis I'm working with experimentally uncharacterized proteins and I only have a AlphaFold prediction. I am interested in using this program. Is it possible? I've been trying to re…