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Questions tagged [alphafold]

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Low confidence score from alphafold2_multimer_v3

I am running alphafold2_multimer_v3 in ColabPro (A100 40 GB GPU) with the following parameters: ...
CoolButNubeBioinformatician's user avatar
2 votes
1 answer
47 views

Can alphafold 2 be used to identify residues important for binding?

I am interested in using AlphaFold2 to identify residues within a homodimer that are important for the protein-protein interaction. I have been able to use ColabFold to produce a predicted dimer ...
user48660's user avatar
3 votes
0 answers
47 views

Oligomer status prediction with Alphafold 2

I am new to using Alphafold 2 and have been primarily using ChimeraX and Colabfold to run some preliminary predictions. I am particularly interested in using AF2 to predict the homo-oligomerization ...
user48660's user avatar
1 vote
0 answers
14 views

Discrepancy between UniProt and AlphaFold data for MlaD domains – Seeking guidance on automating entry sorting based on accurate domain count

Hey fellow researchers, I recently conducted an analysis on the UniProt database, specifically focusing on entries with MlaD domains. After downloading the data and opening it in an Excel file, I ...
Deepankar's user avatar
1 vote
0 answers
59 views

Energy error margin for protein structures

I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their ...
Omar Shehab's user avatar
0 votes
1 answer
62 views

Does AlphaFold actually calculates the fold?

After reading through papers and the code, I'm still not clear if AlphaFold and the likes do actually calculate the 3d structure. My current feeling they are more like information retrieval engines. ...
biocodz's user avatar