Question: Convert to PDB Format from Secondary Strucutre
gravatar for virpatel3
5.3 years ago by
United States
virpatel320 wrote:

I have a sequence of secondary structures in the following format:


I also have the amino acids underneath these structures. Is there any way I can convert this information to the PDB format?



structure convert secondary pdb • 2.2k views
ADD COMMENTlink modified 3.5 years ago by Biostar ♦♦ 20 • written 5.3 years ago by virpatel320

See what are the mandatory fields in PDB file format. Check whether you have necessary information. A small script to make the required format and add dummy values in case of missing information.

I think the 3-D coordinates are only the mandatory feature in PDB file.

ADD REPLYlink modified 5.3 years ago • written 5.3 years ago by geek_y11k

Q. Does the format contain the 3D coordinates? A. Yes - then you can. No - then you cannot.

ADD REPLYlink written 5.3 years ago by Neilfws48k
gravatar for RamRS
5.3 years ago by
Houston, TX
RamRS27k wrote:

Elaborating and generalizing Neilfws's response,

"Converting" secondary structure to 3D structure would be possible only if you knew the 3d coordinates of each atom because there are way too many quirks in protein structure for any piece of software to reliable predict possible 3D structure without homology modeling or extensive simulation. Each residue would need for a dozen assumptions to be made and that increases the number of possible structures exponentially with increasing length.

Generalizing Neil's response, "converting" is only possible when you're stepping to a format that has either the same or lesser information content than the source format. The other way is possible if the additional information is not important, in which case you can substitute dummy values (as with FASTA to FASTQ conversion).

ADD COMMENTlink written 5.3 years ago by RamRS27k
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