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15
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2.3k
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Where does BioPython store information related to various chemical molecules?
protein pdb python biopython
updated 17 months ago by 43k • written 17 months ago by ▴ 20
2
votes
1
reply
483
views
Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?
protein bond amino-acid residue
updated 17 months ago by ▴ 370 • written 17 months ago by ▴ 20
0
votes
3
replies
705
views
What are some tools capable of generating main chain from C-alpha trace only?
protein alpha-carbon pdb
updated 18 months ago by ★ 27k • written 18 months ago by ▴ 20
0
votes
3
replies
983
views
How can I clean a PDB file using VMD or NAMD?
protein namd pdb vmd
updated 18 months ago by ★ 27k • written 18 months ago by ▴ 20
0
votes
0
replies
337
views
How can I compute the performance of an application software?
protein alpha-carbon pdb protein-reconstruction
18 months ago by user366312 ▴ 20
1
vote
5
replies
2.2k
views
how can I compare two PDB files?
protein alpha-carbon pdb
updated 18 months ago by ★ 2.0k • written 18 months ago by ▴ 20
1
vote
7
replies
1.1k
views
What would the items look like if we put them on a length scale?
length-scale scale time-scale biological-process offtopic
updated 22 months ago by ★ 27k • written 22 months ago by ▴ 20
0
votes
1
reply
549
views
What does it mean by "dynamics"?
dynamics protein-dynamics protein
updated 22 months ago by ★ 2.5k • written 22 months ago by ▴ 20
3
votes
2
replies
548
views
Which one is the smallest but the most complex PDB file?
pdb protein
updated 22 months ago by ★ 2.0k • written 22 months ago by ▴ 20
2
votes
1
reply
396
views
Which atoms are not found in protein PDB files?
pdb protein
updated 22 months ago by ★ 2.0k • written 22 months ago by ▴ 20
0
votes
1
reply
520
views
How can I parse alternative atom information in a PDB file?
pdb protein
updated 22 months ago by ★ 2.0k • written 22 months ago by ▴ 20
0
votes
0
replies
374
views
What does it mean by a "site" in the case of a CG model?
coarse-grained modeling simulation
23 months ago by user366312 ▴ 20
3
votes
2
replies
565
views
What do they mean by "multidomain" and "multimetric"?
protein protein-structure protein-structure-prediction
23 months ago by user366312 ▴ 20
4
votes
1
reply
767
views
What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
protein protein-structure protein-structure-prediction
updated 23 months ago by ★ 27k • written 23 months ago by ▴ 20
0
votes
0
replies
401
views
Open issues in protein simulation in MC?
protein protein-structure protein-structure-prediction
23 months ago by user366312 ▴ 20
0
votes
0
replies
383
views
What does it mean by pruning and enrichment in the case of Rosenbluth method?
polymer simulation monte-carlo rosenbluth
2.0 years ago by user366312 ▴ 20
0
votes
0
replies
357
views
Polymer simulation
polymer simulation bead-spring-model monte-carlo
2.0 years ago by user366312 ▴ 20
0
votes
0
replies
243
views
Can you recommend a book on molecular modeling that supplies programming examples?
molecular-modeling
2.0 years ago by user366312 ▴ 20
2
votes
1
reply
484
views
What does it mean by "conformational space"?
protein-structure-prediction protein-structure protein
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 20
3
votes
2
replies
585
views
What does it mean by local structure?
protein-structure proteins
updated 2.1 years ago by ★ 27k • written 2.1 years ago by ▴ 20
0
votes
0
replies
343
views
What is coarse-grained modeling of proteins?
simulation protein modeling
2.1 years ago by user366312 ▴ 20
0
votes
0
replies
298
views
How to represent a summary of disagreement between two secondary structure predictors given predictions for many proteins?
protein-structure-prediction secondary-structure protein-structure protein
2.2 years ago by user366312 ▴ 20
1
vote
6
replies
3.5k
views
How can I list all amino acids in a protein using PyMOL?
pdb pymol
updated 2.2 years ago by ★ 2.0k • written 2.2 years ago by ▴ 20
2
votes
4
replies
920
views
Secondary structure assignment tool.
secondary-structure protein assignment
2.2 years ago by user366312 ▴ 20
1
vote
3
replies
992
views
Can I traverse/enumerate PDB one at a time using a Python script without downloading all of them to my local disk?
python pdb-file proteins
updated 2.5 years ago by 21k • written 2.5 years ago by ▴ 20
0
votes
0
replies
482
views
How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?
proteins hydrogen pdb python
2.5 years ago by user366312 ▴ 20
0
votes
1
reply
647
views
How can I get a list of neighboring Hydrogen atoms of an alpha-carbon?
python biopython protein
updated 2.5 years ago by ★ 27k • written 2.5 years ago by ▴ 20
0
votes
0
replies
698
views
How can I calculate the distance between a C-alpha atom and its hydrogen bond in a protein?
python hydrogen-bonds pdb-file proteins
2.5 years ago by user366312 ▴ 20
0
votes
4
replies
1.5k
views
How can I calculate hydrogen bonds in a specific direction w.r.t. a C-alpha atom in a protein?
python hydrogen-bonds pdb-file proteins
2.5 years ago by user366312 ▴ 20
4
votes
4
replies
944
views
What is the difference between Assignment and Prediction?
protein protein-structure protein-structure-prediction
updated 2.8 years ago by ★ 27k • written 2.8 years ago by ▴ 20
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