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Questions tagged [pdb]

A file format used in structural biology to describe the 3-D coordinates of atoms of a biological structure, often a protein. Can also refer to the Protein Data Bank database, which stores all the submitted biological structures, most of which were obtained using X-ray crystallography.

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5 answers
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How can we find the distance between all residues in a PDB file?

If we have a PDB structrure, how can we find residues physically interacting with each other in space? I know that we must find the distance between residues and if the distance is less than 5-6 ...
Sara's user avatar
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9 votes
5 answers
1k views

Converter between PDB or mmCIF and MMTF

I'd like to test MMTF, a new format for storing biomolecular structures which is promoted by RCSB as a more compact alternative to mmCIF and PDB. From MMTF FAQ: How do I convert a PDBx/mmCIF ...
marcin's user avatar
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7 votes
3 answers
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Read PDB file, extract dihedral angles, modify dihedral angles, reconstruct Cartesian coordinates, and write PDB file

As the title summarizes, I am trying to: Read a PDB file (for example, 1enh.pdb). Extract the backbone dihedral angles (phi, psi). Modify the dihedral angles (phi, ...
epsilone's user avatar
  • 125
5 votes
4 answers
3k views

How to map PDB chains to Uniprot IDs using API services

I have a lot of PDB IDs and I need to get uniprot fasta sequences of these PDB IDs special chains by API services. For example, imagine that I need to get fasta sequence of '1kf6' 'A' chain. The ...
Sara's user avatar
  • 777
5 votes
3 answers
2k views

Best distance parameter for estimating physical interaction between residues in a PDB file

We can calculate the distance between residues in a PDB file regarding different parameters like closest atoms, alpha carbon, beta carbon, centroid and etc. Which one of these parameters are better to ...
Sara's user avatar
  • 777
3 votes
1 answer
5k views

Merge multiple PDB files into a single file

I have several pdb files and each of them corresponds to a domain on a protein. I want to merge these files into one single pdb for the whole protein, and the approach I'm looking for should allow me ...
Morrian Lynn's user avatar
3 votes
2 answers
354 views

How to find/build the evolutionary history of a protein from its sequence?

I'd like to build the evolutionary history of a protein, given its sequence. Namely, given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein as an example: ...
0x90's user avatar
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2 votes
1 answer
56 views

How reliable is Alphafold2 for folding random-coil peptide

I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90). But during actual experiment (e.g. crystallography, ...
neversaint's user avatar
2 votes
3 answers
801 views

Retrieve ID ligand from PDB file

I have thousands of PDB files and I need to extract the following information from each of them: an ID or the name of the small molecule (ligand) present in the complex. Is there a way to do that ...
wrong_path's user avatar
2 votes
4 answers
919 views

How to download ligands for PDB structure

I have some PDB IDs and for every structure, I need all its ligands, so I want to automate the process. The ligands are different for every chain: ...
maciejwww's user avatar
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2 votes
2 answers
1k views

Get a list of PDB ids from a list of sequence protein number?

I am working on a project about phosphorylation, and I am creating a database of some proteins. I have a list of protein accession ids for which I need to get the corresponding PDB file for each one ...
Protocol313's user avatar
1 vote
0 answers
126 views

How can I compute energy from a protein PDB file?

Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in the file. How can I do that? Sometimes people suggest using the ...
user366312's user avatar
1 vote
2 answers
3k views

Generating PDB file for custom DNA sequence

I asked this question in biology.stack exchange and was referred to this community. I am going to request migration for this question. https://biology.stackexchange.com/q/105024/67415 I want a PDB ...
dnalectronics's user avatar
1 vote
1 answer
525 views

How to calculate RMSD and binding energy from the already docked ligand-receptor

I have the following PDB file that looks like this. It is downloadable here. This PDB already contains ligand and receptor together. The red molecule is the ligand and the yellow is the receptor. They'...
littleworth's user avatar
0 votes
1 answer
213 views

Error pasing the following line in pdb

I converted an .sdf file containing around 50,000 anti-viral agents to individual .pdb files using OpenBabel. However, when I tried opening the .pdb files with Autodock I kept getting the error below. ...
Shahbaaz's user avatar