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Comment: Comment: Where does BioPython store information related to various chemical molecules?
2.8 years ago by user366312 ▴ 20
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3.5k
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Comment: Comment: Where does BioPython store information related to various chemical molecules?
2.8 years ago by user366312 ▴ 20
0
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0
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3.5k
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Comment: Comment: Where does BioPython store information related to various chemical molecules?
2.8 years ago by user366312 ▴ 20
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15
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3.5k
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Where does BioPython store information related to various chemical molecules?
protein pdb python biopython
updated 2.8 years ago by 45k • written 2.8 years ago by ▴ 20
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Comment: Comment: Where does BioPython store information related to various chemical molecules?
2.8 years ago by user366312 ▴ 20
0
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1
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3.5k
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Comment: Comment: Where does BioPython store information related to various chemical molecules?
2.8 years ago by user366312 ▴ 20
0
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1
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3.5k
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Comment: Comment: Where does BioPython store information related to various chemical molecules?
2.8 years ago by user366312 ▴ 20
2
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1
reply
734
views
Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?
protein bond amino-acid residue
updated 2.8 years ago by ▴ 380 • written 2.8 years ago by ▴ 20
0
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1
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1.1k
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Comment: Comment: What are some tools capable of generating main chain from C-alpha trace only?
2.9 years ago by user366312 ▴ 20
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3
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1.1k
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What are some tools capable of generating main chain from C-alpha trace only?
protein alpha-carbon pdb
updated 2.9 years ago by ★ 29k • written 2.9 years ago by ▴ 20
0
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1
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1.5k
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Comment: Comment: How can I clean a PDB file using VMD or NAMD?
2.9 years ago by user366312 ▴ 20
0
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3
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1.5k
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How can I clean a PDB file using VMD or NAMD?
protein namd pdb vmd
updated 2.9 years ago by ★ 29k • written 2.9 years ago by ▴ 20
0
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0
replies
507
views
How can I compute the performance of an application software?
protein alpha-carbon pdb protein-reconstruction
2.9 years ago by user366312 ▴ 20
0
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1
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3.5k
views
Comment: Comment: how can I compare two PDB files?
2.9 years ago by user366312 ▴ 20
1
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5
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3.5k
views
how can I compare two PDB files?
protein alpha-carbon pdb
updated 2.9 years ago by ★ 2.1k • written 2.9 years ago by ▴ 20
1
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7
replies
2.0k
views
What would the items look like if we put them on a length scale?
length-scale scale time-scale biological-process offtopic
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 20
0
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1
reply
811
views
What does it mean by "dynamics"?
dynamics protein-dynamics protein
updated 3.2 years ago by ★ 2.9k • written 3.2 years ago by ▴ 20
3
votes
2
replies
1.0k
views
Which one is the smallest but the most complex PDB file?
pdb protein
updated 3.2 years ago by ★ 2.1k • written 3.2 years ago by ▴ 20
2
votes
1
reply
676
views
Which atoms are not found in protein PDB files?
pdb protein
updated 3.2 years ago by ★ 2.1k • written 3.2 years ago by ▴ 20
0
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1
reply
830
views
How can I parse alternative atom information in a PDB file?
pdb protein
updated 3.2 years ago by ★ 2.1k • written 3.2 years ago by ▴ 20
0
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0
replies
582
views
What does it mean by a "site" in the case of a CG model?
coarse-grained modeling simulation
3.3 years ago by user366312 ▴ 20
0
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0
replies
617
views
Forum: Can Bioinformatics be used in developing a product?
product company business
updated 2.7 years ago by 45k • written 3.3 years ago by ▴ 20
1
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0
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948
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Comment: Comment: What do they mean by "multidomain" and "multimetric"?
3.3 years ago by user366312 ▴ 20
3
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2
replies
948
views
What do they mean by "multidomain" and "multimetric"?
protein protein-structure protein-structure-prediction
3.3 years ago by user366312 ▴ 20
4
votes
1
reply
1.1k
views
What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
protein protein-structure protein-structure-prediction
updated 3.3 years ago by ★ 29k • written 3.3 years ago by ▴ 20
0
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0
replies
582
views
Open issues in protein simulation in MC?
protein protein-structure protein-structure-prediction
3.3 years ago by user366312 ▴ 20
0
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0
replies
564
views
What does it mean by pruning and enrichment in the case of Rosenbluth method?
polymer simulation monte-carlo rosenbluth
3.4 years ago by user366312 ▴ 20
0
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0
replies
528
views
Polymer simulation
polymer simulation bead-spring-model monte-carlo
3.4 years ago by user366312 ▴ 20
0
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0
replies
370
views
Can you recommend a book on molecular modeling that supplies programming examples?
molecular-modeling
3.4 years ago by user366312 ▴ 20
2
votes
1
reply
966
views
What does it mean by "conformational space"?
protein-structure-prediction protein-structure protein
updated 3.4 years ago by ★ 1.7k • written 3.4 years ago by ▴ 20
3
votes
2
replies
1.0k
views
What does it mean by local structure?
protein-structure proteins
updated 3.4 years ago by ★ 29k • written 3.4 years ago by ▴ 20
0
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0
replies
534
views
What is coarse-grained modeling of proteins?
simulation protein modeling
3.4 years ago by user366312 ▴ 20
0
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0
replies
489
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
3.5 years ago by user366312 ▴ 20
0
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1
reply
6.4k
views
Comment: Comment: How can I list all amino acids in a protein using PyMOL?
3.5 years ago by user366312 ▴ 20
0
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1
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6.4k
views
Comment: Comment: How can I list all amino acids in a protein using PyMOL?
3.5 years ago by user366312 ▴ 20
1
vote
6
replies
6.4k
views
How can I list all amino acids in a protein using PyMOL?
pdb pymol
updated 3.5 years ago by ★ 2.1k • written 3.5 years ago by ▴ 20
0
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0
replies
1.4k
views
Comment: Comment: Secondary structure assignment tool.
3.5 years ago by user366312 ▴ 20
0
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1
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1.4k
views
Comment: Comment: Secondary structure assignment tool.
3.5 years ago by user366312 ▴ 20
2
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4
replies
1.4k
views
Secondary structure assignment tool.
secondary-structure protein assignment
3.5 years ago by user366312 ▴ 20
0
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1
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1.4k
views
Comment: Comment: Can I traverse/enumerate PDB one at a time using a Python script without downloa
3.8 years ago by user366312 ▴ 20
1
vote
3
replies
1.4k
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 3.8 years ago by 22k • written 3.8 years ago by ▴ 20
0
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0
replies
670
views
How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?
proteins hydrogen pdb python
3.8 years ago by user366312 ▴ 20
0
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1
reply
869
views
How can I get a list of neighboring Hydrogen atoms of an alpha-carbon?
python biopython protein
updated 3.9 years ago by ★ 29k • written 3.9 years ago by ▴ 20
0
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0
replies
943
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
3.9 years ago by user366312 ▴ 20
0
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0
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2.1k
views
Comment: Comment: How can I calculate hydrogen bonds in a specific direction w.r.t. a C-alpha atom
3.9 years ago by user366312 ▴ 20
0
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1
reply
2.1k
views
Comment: Comment: How can I calculate hydrogen bonds in a specific direction w.r.t. a C-alpha atom
3.9 years ago by user366312 ▴ 20
0
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4
replies
2.1k
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
3.9 years ago by user366312 ▴ 20
4
votes
4
replies
1.3k
views
What is the difference between Assignment and Prediction?
protein protein-structure protein-structure-prediction
updated 4.2 years ago by ★ 29k • written 4.2 years ago by ▴ 20
0
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1
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1.3k
views
Comment: Comment: What is the difference between Assignment and Prediction?
4.2 years ago by user366312 ▴ 20
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