New answers tagged protein-structure
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__♦
- 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 ...
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 ...
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 ...
Top 50 recent answers are included
Related Tags
protein-structure × 178proteins × 52
pdb × 48
python × 26
structural-biology × 18
docking × 17
3d-structure × 16
pymol × 10
protein-protein-interaction × 10
sequence-alignment × 8
database × 6
visualization × 5
modelling × 5
computational-biochemistry × 5
secondary-structure × 5
fasta × 4
gene × 4
phylogenetics × 4
biopython × 4
covid-19 × 4
r × 3
sequence-analysis × 3
bash × 3
sars-cov-2 × 3
interactions × 3