Questions tagged [biopython]

Questions about using Biopython to solve a biological programming task.

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RMSD / Tm metric for comparing local molecular structure similarity?

I would like to compare two molecular (protein) structures, but rather than comparing the total, global structures against themselves to yield an RMSD score (which would be straightforward with a ...
asimov's user avatar
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0 votes
0 answers
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How do i find and download targets of drugs which are in DrugBank?

Recently, I am focused on drugs and their interactions. But since I am new in this field, using experts experience would help me a lot. I have downloaded DrugBank xml file from DrugBank website and ...
Orca's user avatar
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1 vote
1 answer
55 views

Can one use DSSP (secondary structure assignment) for short peptides of size 6, 10 and 18?

I have large number of PDB files of peptides of size 6, 10 and 18. I wanted to cluster the peptide structure based on the secondary structure. I used DSSP in mdtraj module in python to assign DSSP ...
vigneshwaran kannan's user avatar
0 votes
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31 views

Tools for modelling and visualizing growth of cells

I am looking for a program/GUI app/package that would help me do simulations for cell growth. I have a microscopic mathematical model, and the scenario is basically the following: I start with a rod-...
Fabulini's user avatar
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0 answers
134 views

conversion of distance matrices to pdb/coordinates

I am currently facing two transformational issues. Suppose I am given a protein's residue sequence and calpha distance matrix; is there a way to generate the 3d coordinates of the protein's residues ...
GTOgod's user avatar
  • 109
2 votes
0 answers
70 views

Phylogenetic tree with tagging

I'm working for a software company. For one of our projects, we need software to cluster nodes in a phylogenetic tree by a certain kind of similarity and give them a user-defined tag. Preferably, the ...
Sceada's user avatar
  • 121
0 votes
1 answer
145 views

How to convert PDB file of Amino Acids to rotamer tuples list of all AAs instances

Either by Python command, or via specific application (like Chimera) publicly available. Please provide example or link to one of. I have to detect AA location within MAP (density) 3D matrix. And to ...
Leon Kigelman's user avatar
4 votes
3 answers
232 views

Identifiying a conserved residue in multiple PDB structures

I have a few hundred PDB structures of the same protein, and I need to identify a specific conserved residue in all of them. Originally I wanted to extract the sequences from the PDB files with ...
user27874's user avatar
4 votes
3 answers
1k views

Construct Phylogeny form Edgelist

I am working on large scale biodiversity simulations and have collected a lot of data on simulated phylogenies. I have a list of child-parent edgelist species in the form: ...
Sanalphatau's user avatar
3 votes
2 answers
686 views

Change Genbank entry date with Biopython

I can create a new Genbank record in Biopython with the following code: ...
TheChymera's user avatar
  • 1,316
2 votes
2 answers
2k views

View ABI chromatogram plots with python

I would like to view the chromatogram traces from a few ABI (.ab1) files. I would prefer to use python for this, or a function with python bindings, or at least some open source package such as EMBOSS....
TheChymera's user avatar
  • 1,316
14 votes
2 answers
537 views

Biopython - Big Discrepancy Calculating RNA melting Temperature over Literature

I experience big discrepancies when calculating melting temperature of RNA 7-mers with Biopython over values generated by a popular algorithm. I tried the nearest neighbour algorithm with RNA and ...
pykong's user avatar
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