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5 votes
2 answers
341 views

Why does it require 4 vectors to calculate a torsion angle?

4 votes
1 answer
46 views

Are the information stored in the PBD files in the protein data bank complete or incomplete?

4 votes
1 answer
167 views

Which atoms are not found in protein PDB files?

4 votes
1 answer
378 views

Why do we need to find minimum energy in a protein chain?

3 votes
1 answer
68 views

How can I parse alternative atom information?

3 votes
2 answers
56 views

Example of a small but moderately complex PDB file?

3 votes
1 answer
95 views

What is DSSP algorithm for?

3 votes
3 answers
177 views

Can I traverse/enumerate PDB one at a time using a Python script without downloading all of them to my local disk?

3 votes
2 answers
241 views

What is protein secondary structure assignment?

3 votes
1 answer
76 views

How are tertiary protein structures represented in computers?

3 votes
2 answers
52 views

Algorithm for counting neighbors

2 votes
2 answers
2k views

How can I programmatically add Hydrogen to a PDB structure using BioPython?

2 votes
0 answers
60 views

Secondary structure assignment tool

2 votes
0 answers
37 views

What is coarse-grained modeling of proteins?

1 vote
3 answers
533 views

How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?

1 vote
1 answer
61 views

What is the cutoff distance in this algorithm?

1 vote
1 answer
327 views

What is the basic difference between a protein and a ligand?

1 vote
0 answers
88 views

How can I calculate the radius of a residue?

1 vote
1 answer
61 views

What do these characters mean in a PDB file?

1 vote
2 answers
32 views

Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?

1 vote
1 answer
50 views

Why am I not being able to detect all the bonds in a residue?

1 vote
1 answer
40 views

What is changed in this PDB file?

1 vote
0 answers
105 views

When does a 2D histogram / heatmap take a circular shape?

1 vote
1 answer
102 views

What does it mean by a Local Coordinate in the case of protein chains?

1 vote
1 answer
113 views

How can I clean a PDB file using VMD or NAMD?

1 vote
0 answers
12 views

How can I use REMO tool to generate seq.dat and seq.txt files?

1 vote
1 answer
46 views

What options should I explore to improve the output of the protein reconstruction?

1 vote
1 answer
381 views

How can I list all amino acids in a protein using PyMOL?

1 vote
1 answer
904 views

How can I calculate the distances between two specific residues of a protein from a PDB file?

1 vote
0 answers
108 views

How can I compute energy from a protein PDB file?