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 to select high quality structures from the Protein Data Bank?
Models of structures deposited in the Protein Data Bank vary in the quality, depending both on the data quality and expertise and patience of the person who built the model. Is there a well-accepted ...
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How to extract RNA sequence and secondary structure restrains from a PDB file
I'm trying to find a programmatic way to automatically extract the following information from a PDB file:
RNA sequence
Secondary structure restraints in bracket format, e.g. ...
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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 ...
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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 ...
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PDB format: remark number for free text
I would like to add a text to PDB files that I'm processing with my tool, rna-pdb-tools. Someone points that the way I'm using it right now it's not correct (https://github.com/mmagnus/rna-pdb-tools/...
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Is there a standard way to clean a PDB file and re-number its residues?
Is there a pre-existing tool which will tidy up the numbering of a PDB file?
Firstly, I would like to re-number the residues on inserts to make the icode an actual residue in the chain (by that I ...
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How to measure or assign hydrophobicity score values to individual amino acids of a PDB structure?
I want measure the hydrophobicity of each amino acid within a PDB structure file. Since I have the PDB file I want to consider the 3D information, rather than sequence-only measures such as GRAVY.
I ...
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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, ...
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How to get all PDB homologs from Uniprot (mapping + BLAST)?
I'd like to create a dataset consisting of all sequences which are either present in the PDB, or whose homolog is present in the PDB. In other words, any sequence in the PDB or any sequence related to ...
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BinaryCIF vs MMTF formats, which one to choose?
Both file formats are advertised as more memory/parsing efficent than old PDB format and its successor mmCIF format, but I can't understand the context (I'm a developer, but pretty new to the field of ...
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Extract residue sequence from pdb file (in biopython, but open to recommendations)
I'm new to Biopython and I'd like to extract the sequence of residues from a pdb file.
My two questions are:
What is the simplest way to do this? (Esp. when there is more than one sequence)
and
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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 ...
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BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure
I am using the internal_coords module from BioPython in order to compare dihedral angles of two different conformations of the same protein. The conformations are ...
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If I modify a PDB file with a specific mutation, how to minimize energy?
I have a series of proteins that are all phylogenetically related. Only one of this proteins is currently X-ray crystallized.
Is it valid to modify the reference PDB file (I mean by hand) to match ...
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What is a sensible forcefield choice for membrane proteins when using PDB2PQR?
I am generating PQR files for a membrane protein that is almost entirely buried in the membrane. The goal is to calculate the electrostatic charge across the surface of the protein. There are no ...
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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 ...
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What is the aim of insertion codes in the pdb file format?
In PDB file we always see insertion codes (ic) in a few proteins. Could anybody please tell me why it has been added in structure and what is the aim of that ???
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Are the information stored in the PBD files in the protein data bank complete or incomplete?
I know that there are thousands of PDB files stored in Protein Data Banks.
Are all these files complete in terms of the information they store?
If YES, do the individual files get updated from time to ...
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PDB codes for misfolded proteins?
I'm searching for PDB code examples for "healthy proteins" and misfolded ones, so I can compare the 3D structure.
I'd prefer pairs of a "protein misfolding disease", but could be any. Can I find such ...
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Which atoms are not found in protein PDB files?
I am developing an educational Bioinformatics framework, I need to know
Which atoms are absolutely not found in any PDB files?
in the following list -
Atomic radii of the elements (data page)
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Retrieval of genomic position by using biomaRt package
I have a list of several protein names, their primary gene name and their amino acid sequence (as extracted from the 'SEQRES' section in their corresponding PDB files).
I'm looking for the genomic ...
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Cross-reference with PDB database
I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those ...
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Biopython: resseq doesn't match pdb file
I have a PDB file, and I need to extract its residue sequence numbers (resSeq's). Based on manual inspection of the first few lines of the PDB file (pasted below), I would think that resSeq's should ...
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What is the correct method of identifying the interacting residues for specific molecular docking?
I'm trying to do a specific molecular docking using Autodock Vina in PyRx. So, one way to do that is to mark all of the interacting residues and make sure the grid box encompasses all of that ...
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What is the function of the heteroatoms
I am trying to make a prediction application using the sequence of proteins.
If we think about the 6COU protein, I'm running the code below
...
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Can I traverse/enumerate PDB one at a time using a Python script without downloading all of them to my local disk?
What would be the total size of all PDB files in RCSB?
Can I traverse/enumerate them one at a time using a Python script without downloading all of them to my local disk?
If YES, what would be the ...
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Example of a small but moderately complex PDB file?
I am developing a bioinformatics framework only for learning purposes. I want to calculate --
dihedral angles
detect H, E, and C components
detect Hydrogen bonds
etc.
Therefore, I want a PDB file ...
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PDB file downloading: pymol automation vs. manual
I automated a PDB download using a Pymol script (below)
...
M__♦
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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:
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How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?
I encountered the dichotomy in the context of PDBx/mmcif files, say, 6OSQ: each chain has a
_entity_poly.pdbx_seq_one_letter_code...
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How can I parse alternative atom information?
I am trying to parse PDB files.
Say, a PDB file has the following data:
...
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How to select only RNA with Hetero atoms from pdb file with python?
I'm trying to separate RNA from protein in a complex protein/RNA PDB file and I want all RNA info with the hetero atoms in between the bases BUT without H20 etc. In short I want RNA part of pdb file ...
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Determining position of side chain hydrogen in glycine residues from coordinates of backbone atoms
I have a dataset of pdb-format protein structure decoys/models generated by tertiary structure prediction programs. Many of these are missing hydrogen atoms.
Specifically, I'd like to determine the ...
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Is there a tool that can take a protein's amino acid sequence and would display it's locus on the genome?
I have the UNIPROT IDs, PDB IDs and FASTA files of several known proteins. I am looking for a tool that can take as input the protein's amino acid sequence and display the coding nucleotides of those ...
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Can you query the RCSB PDB API with a ligand and return the IDs of all entries in which it appears as a free ligand?
If you're looking at the entry for a ligand, for example, adenosine, there's a link on the webpage to entries for which this entry exists as a free ligand.
However, I want to access this via the API ...
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How to extract a list of hydrogen bonds from a PDB?
I am analyzing the 7VF2 structure, from the RCSB-database. I noticed that some residues belonging to one of its chains interact with the other chains that are present within the assembly. My question ...
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Relationship between entries for same UniProt Id
I was playing around, looking at some AlphaFold predictions for certain proteins and I realized that sometimes the sequences of aminoacid look very different for the same UniProt id. For example, 15C8 ...
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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 ...
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finding RNA-protein physical interaction
We all know that for physical protein-protein interaction, we need to find the distance between residues from PDB file of that interaction (finding distance between carbon alpha, carbon beta or ...
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How do I find a list of PDB structures bound to a peptide inhibitor or peptide-like inhibitor?
I looked up existing databases but ones like iPPI-DB or enter link description here either provide non-peptide inhibitors or only sequences. I need structures of proteins bound to other proteins, the ...
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getting KeyError on certain residues in BioPython: ATOM vs. HETATM lines
When I want to load atoms for residuum (' ', 85, ' ') in chain A for protein 3tmm with structure[0][chain_id][residue], but I'm ...
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which secondary structure assignment algorithm is used by PDB?
older releases of PDB used to specify DSSP as the 2ary structure assignment algorithm used in PDB, right now no algorithm is explicitly stated. Where can I find a reference for it in the database?
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How to draw a 3d structure using 3d coordinates from pdb file?
I am trying to create a 3d structure from 3d coordinated from a pdb file.
I am trying to draw 3d coordinates from pdb file "ATOM 1 N VAL A 14 22.692 -27.591 -39.402" and using webgl ...
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How to extract subset of protein structure (PDB format) file based on a subsequence of that protein
I looking at a particular protein structure called 2LY4 accessible from RSCB PDB website.
The corresponding fasta sequence for that structure is this:
...
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Is there a way to get a list of all PDB IDs for proteins with crystal structure information?
I would like to download all the PDB files which have crystal structure information in them. But the query builder seems to require me to enter the PDB IDs manually.
Is there a way to get a list of ...
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Creating a PDB from a figure in paper
I want to create a PDB file of a drug that is given in a paper.
Can somebody share a tutorial or similar resources for a beginner-level user?
Thank you.
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How to find a homolog that has a PDB structure available
I tried to find a homolog that has a PDB structure available so I can use this PDB file for comparative modeling. I ran a BLAST search but none of the search results seemed to have a known structure. ...
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Using R to import specific records from a PDB file
I'm using R and I'm trying to import specific records from a PDB file (e.g. HETNAM, HETSYN). Unfortunately, it seems the ...
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How to read the "SEQRES" section from a PDB file, using R
I'm using R and its Rpdb package to work with PDB files. I use the read.pdb function but, nevertheless, I couldn't find the argument which will allow me to view the ...
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What does it mean when PDB lists multiple organisms for the same structure?
I'm browsing through ribosomes which have been modeled with Cryoem on PDB and am pretty confused by the fact that for some, PDB, or rather the authors of the deposition probably, put multiple ...
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