New answers tagged

0 votes

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__'s user avatar
  • 11.9k
0 votes

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 ...
pippo1980's user avatar
  • 955
2 votes

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 ...
Maximilian Press's user avatar
1 vote

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 ...
marcin's user avatar
  • 1,261

Top 50 recent answers are included