New answers tagged protein-structure
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Does AlphaFold actually calculates the fold?
Alphafold calculates the "folds" throughout a protein, thus its protein structural prediction. It uses convolution-based calculation, which is a modification of co-variance. The reason it ...
M__♦
- 11.9k
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BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure
OK , visualizing both proteins in PyMOL , using set cartoon_gap_cutoff = 0 ,
I get :
Apparently the two conformations , have more than one difference in various ...
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If I modify a PDB file with a specific mutation, how to minimize energy?
The previous answers suggest Chimera and FoldX, which require a license for commercial use.
Commercial users can use pdbfixer or a similar tool to perform mutations (using e.g. applyMutation in the ...
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Downloading a list of all RCSB-PDB entries
Did you try RCSB sequence similarity search?
These two announcement highlight the options you ask about:
Improved Searching with New Sequence Identity Cutoff (2017)
Remove Redundancy in Search ...
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