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Hey, just a thought. You could probably do something similar with the new gLM2 and Sergey's "Categorical Jacobian" method, and this would be very useful for filtering binders designed by RFdiffusion, …
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Hi,
First of all, thank you for such wonderful tool. I'm working with proteins translated from new ORFs and I predicted that the new protein interact with another protein, say for e.g. protein X. N…
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Dear Developers
I have 13 PDB files obtained from AlphaFold database and we suspect these 13 PDB form a complex. We thought of performing the protein-protein docking to check this using haddock3 bu…
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We've received a request to update the field related to "Has this gene or genes been implicated in the above disease?" in the Protein Interactions section of the GCI. Example: https://curation-test.cl…
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Hi,
thank you for sharing your script of doing protein docking.
I am currently working with protein-protein interaction, and am trying to use your codes on my alphafold3 predicted structure.
Ho…
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[Rhea](https://www.rhea-db.org/) is a database of "chemical and transport reactions of biological interest". Mappings between chemical compounds and Rhea IDs is available through mychem.info (and will…
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This software is very impressive!
Is it possible to add a feature for direct upload of PDB files or ligand sdf/mol2 files for protein-ligand binding prediction or protein-proterin binding prediction…
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I encountered a problem when using YASARA to calculate hydrogen bonds, PIPI bonds, ca-pi bonds and saltbrige between proteins and small molecules.
My yasara version is: 22.5.22.
The command I used…
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Hi, recently I buy lot of memory to do bigger structure interactions, and I have the impression Alpha Pulldown cannot take more than 10 proteins (here 20). Maybe it's cause the name is too long ?
T…
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From string-db.org, will be used for constructing gene-gene edges of our graph.
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