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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42 views

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've managed to get the 3d coordinates from a pdb file but i don't know the exact logic that is used to create 3d structure ...
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How to get 2d/3d structural coordinates from a PDB file?

Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file. I have looked a believe that the coordinates are in below line: ...
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PDB: Download all biological assemblies

I was wondering if it is possible to download all biological assemblies from the PDB at once (so not the standard asymmetrical files). For example, I want a file containing the coordinates of all ...
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Regularly extract models from multimodel PDB file

I have a huge text file (10GB) formatted as follow (multimodel PDB file): ...
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How to calculate various properties of a protein structure per atom using PDB2PQR and Rosetta tools (or any other tools)?

Currently, I am implementing a descriptor of protein structure and would like to calculate properties per atoms like charges, hydrophobicity, hydrogen bond donors / acceptors, hydrophobicity, ...
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Generate multiple output file based on editing operations done on PDB input files stored in same directory

I have hundred PDB files that I want to loop through in the directory and carry out some editing operations and save them as new PDB files using R script. Right now, I am using the following code but ...
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61 views

OpenAPI-Generator Python Client Instructions Examples

Trying to learn a little bit of Python and Biopython I ended up figuring out what a Rest API is when the RCSB PDB repository released its new Rest API. I tried to retrieve info from the PDB repository ...
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FASTA and PDB: How to specify chain?

For proteins that have multiple chains (e.g., 1EMS), is there an easy way to specify which chain I want to use for blastp? I cannot imagine that I am the first person to have this problem, but so far ...
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I have used TER to break the long bonds of a chain in my PDB

I’m now not sure what I need to alter in my PDB to get it to work in leap. I know breaking the bonds turns the formerly connected residues into terminal residues. It keeps saying that 3 of my atoms no ...
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Mutated residue number shown wrong in foldX yasara

I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
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I am trying to run nab to create the pdb file but it isn`t working (AMBER)

Here is the input file for nab: molecule m; m = arna( "gcuucuucuucuucgc" ); putpdb( "lr16.pdb", m, "-wwpdb -nocid -tr"); I am trying to run nab to create the pdb file ...
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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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.cif .pdb conversion with python

can you please give me an advice how to convert .cif files into .pdb preferably using python? Thanks in advance! Best, Balint Biro
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How many entries in PDB have SS bonds?

Is there a way to figure out what percentage of entries in PDB have SS bonds? In addition, what other types of bonds in PDB may be worth looking into (not H bonds)?
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527 views

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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Extract only the amino acid residues on the surface of protein structure data

I'd like to use protein structure data from PDBs visualized by Chimera to do two things. I'd be happy to learn the appropriate tools and methods. ・Mapping information about amino acids present on ...
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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. ...
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.SDF file to .PDB file

I am currently working on identifying effective antiviral compounds against the corona virus. I have downloaded the Covid-19 AntiViral Candidate Compounds Dataset from the www.cas.org webpage, the ...
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Protein PDB/CIF text file reader that can fold a same section into one line

Is there a software that can recognise the protein PDB/CIF files, and fold multiple lines of a same section into one line, so that it is easier to handle? I need to understand the format in CIF so as ...
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29 views

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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Can I automate CLUSTALO and output alignment sequence identity?

I've detected homology between targets of ligands in drugbank and proteins in the proteome of a pathogen. I've parsed the output very rudimentary and calculated my query coverage. This exists in an ...
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288 views

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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how to generate structure file from blast results of an input sequence

I have tried to incorporate blast in my application using biopython.i could extract the blast results but now i want to extract the structure file corresponding matches. My code is : ...
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465 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 ...
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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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Get nucleic acids' chain names from PDB API

There is a place in my pipeline where I call PDB's API with a ribosomal id to get all the subchains of that molecule programmatically I'd like to separate subchains that are proteins from nucleic ...
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119 views

Looking for a way to download all pdb files that detail a protein-drug complex

I am looking for a way to download all pdb files that detail a protein-drug complex. While I could download the entirety of the pdb and search manually (or maybe write a script to discard all ...
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How to generate conformations for a ligand for in silico screening?

I have multiple ligands (in pdb format) which I want to try and dock to various proteins. But for each ligand I have only a single conformation (by which I meant the spatial relationship between it's ...
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79 views

Can foldx position-scan produce different result with different lists of mutations?

I am running foldx position scan for GFPmut2 (PDB: 6GO9) and I use a config file with the following template: ...
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42 views

Download protein structure from gene name

I have a list of gene name, I want to download and save each protein 3D structure corresponding to each gene name.
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I have a list of protein targets. How to get structural data (atomic coordinate) from PDB?

I have a list of around 500 protein targets (human). I only have their protein symbols. As an example: EGFR AR FOXA1 CXCR3 ... I want to get structural data (atomic coordinate) from PDB (Protein ...
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274 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
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82 views

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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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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71 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 ...
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How to find Wild Type (WT) protein structure on Protein Data Bank (PDB)?

Currently, I am working on Galactose oxidase enzyme for protein docking and I am totally new to it. I have to study how mutation on specific residue will make mutated galactose oxidase better than the ...
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92 views

Preparing PDB file for modeling with Swiss-Model

I recently starting studying bioinformatics and have a question. I need to build a model of protein using Swiss-Model. First, I need to download a protein record from PDB (for example, 2HZI), then I ...
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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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106 views

Reconstruct a protein's 3D structure from a pair-wise distance matrix

What is a good method to reconstruct a protein's 3D structure from a pair-wise distance matrix of residues? I think the question is self-explanatory. I know of this method but it seems that it uses ...
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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 ...
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1answer
165 views

Plotting Ramachandran Plot from more than one PDB file

I want to plot a Ramachandran Plot for around 5000 PDB files in python that is saved in a folder in my system. I am searching for a way to make it without accessing each file by hard-coding each file ...
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112 views

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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Which secondary structure prediction algorithms don't query the PDB/DSSP for known homologous sequences?

There are several secondary structure prediction algorithms. I am interested in the algorithms which predict secondary structure without accessing the PDB to cheat by using the DSSP or STRIDE entry ...
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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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160 views

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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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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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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Automating download of results of Drug and Drug Target Mapping

The drug and drug target mapping tool shows the top 3 PDB IDs for each drug based on the drug target sequence similarity search and ligand id search. Is there a way to get all the PDB ids of the drug-...
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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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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 ...