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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How can I search globular proteins by residue count in the RCSB databse?
I want to find some globular proteins with some of the longest individual chains that have all three types of secondary structures,, namely helix, sheet, and loop.
So, I tried the following search:
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Python/R/bash script to ease the comparison of different protein complexes in PDB
I would like to create a table of comparison among similar protein complexes from the pdb.
This would be based on their numbers of proteins and the presence of each protein.
Is there any way like ...
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Why do we need seondary structure detection algorithms?
There are many secondary structure prediction and assignment algorithms (e.g., DSSP, STRIDE, etc.) available.
On the other hand, I see that PDB files have secondary structure information available in ...
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How can I check if a PDB file is incomplete?
One of the requirements of simulating the protein chain is to check for missing atoms or residues. I.e., using software tools to identify (and, if necessary, model) any missing regions.
How can I ...
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Protein symmetry classification from PDB data
Given the PDB or mmCIF information of a homomeric protein assembly whose global symmetry is unknown, how might one design an algorithm to find which point group symmetry class it belongs to (cyclic $...
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Does the `mmcif/pdb` format store atomic coordinates in units of Ångstrom, nanometers or something else?
I was surprised as to how hard it was to find a reference on this among the docs.
Does the Protein Data Bank mmcif/pdb-x archival format use Angstrom to specify cartesian x,y,z coordinates of atoms or ...
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(Complete) Stuctural Models of Antibodies: Combining Fc and Fab from pdb to Build Hinge Region? Or what?
I'm a newcomer to the field of antibodies, and I'm seeking guidance on obtaining 3D structures for my molecular simulations. After browsing the PDB databank, I noticed that there are Fab and Fc ...
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How to add charges to a PDB file?
I did some calculations using a PDB file as input. As a result, I got a file with the atomic partial charges (only the values in one column, no other information) and the output PDB file structure ...
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Downloading a list of all RCSB-PDB entries
I'm trying to download a list of all of the non-redundant protein chain IDs in the RSCB-PDB (not the actual FASTA entries, just the IDs), filtered by some % identity.
Does anyone know how to do this? ...
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Ramachandran Plot for specific amino acids in a pdb file
Does anyone know of a Ramachandran plot server (URL please) that allows you to display, for example, just the leucine residues in a protein structure rather than displaying all the amino acids in the ...
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How does BioJava retrieve bond information from a PDB file?
How can I compute energy from a protein PDB file?
I asked the above question.
Then I thought, Why don't I check how BioJava obtains bond information from a protein PDB file?
Surprisingly, BioJava's ...
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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 ...
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Align two different structures with respect to their active sites or heme cofactor
I have two enzymes, with heme cofactors. but their overall structure is very different.
I use Pymol regularly to visualize protein pdb structures.
I want to align both structures, but the structures ...
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Good practices for doing sanity checks when parsing multiple PDB files
This is my first time posting to stack exchange, as well as to using data-driven approaches, so please correct me if my questions is not clear enough.
I am trying to parse 200+ .pdb files to extract ...
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Is there any python module to assign secondary structures which includes both Polyprolene region as well as individual strand as well?
I wanted to assign secondary structure to set of pdb files. However, DSSP and STRIDE cannot assign for single peptides if it is falling inside single long beta strand or polyprolene region as it does ...
