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 get the Scientific/Organism name by using pdb id

I am trying to get ScientificName (CommonName) of protein by using pdb id. For example, 6hx5 is ...
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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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How to extract residues from specific chain of interest from multiple pdb files?

I'm new to biopython & I'm trying to extract residues from specific chain of each file from a list of 316 pdb files. Eg: 1d8t has four chains A, B, C & D of which my interest is to extract ...
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How to have in home alphafold predicted structure pdbs converted to mmCIF files in line with alphafold standards?

I am using AlphaFold to predict some protein structures of interest, not covered in their DB yet. What I am obtaining are PDB files with atom coordinates like in the line below with no further ...
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Repeating indexes of atoms in PDB file

I have a PDB file in which the indexes of atoms are repeated (or better say refreshed) every 99999. I am using MDtraj software to analyze this pdf file, so these repeating indexes cause some problems. ...
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locating hydrocarbon in PDB file

Does everyone know how can I understand whether my PDB file has a Hydrocarbon or not? and how to locate it using VMD
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Protein-Ligand in PDB

I am a newbie in bioinformatics. In PDB, while searching for proteins, I sometimes get protein with ligand, such as PDB ID 1J1Z. In cases I get pure protein structure, in some cases I get protein-with ...
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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, ...
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Active sites of the query protein does not align with the top hit using HHpred

I am having difficulties with an alignment on HHpred and was wondering if anyone had any answer to the following: I am trying to align my protein (PDB 2VU9, a Botulinum Neurotoxin Type a) with one of ...
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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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How can I convert protein distance maps and sequences to a pdb files?

How can I convert protein distance maps and sequences to pdb files? For the same problem, in the case of a model predicting the structure of a protein, such as AlphaFold, how do we convert the ...
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How can I list all amino acids in a protein using PyMOL?

What is the command in PyMOL for listing all the amino acids in a specific protein, say, 1a62.pdb?
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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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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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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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PDBQT file format

I am trying to understand the source code of the AutoDock Vina, but as I am new to the field of Bioinformatics it is a little hard to understand. It seems like they are using a tree data structure to ...
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Extracting and analyzing structure data of multiple proteins from PDB using Python

I am new to programming and I am given the task to extract structural data of soluble proteins from PDB and then shortlist the soluble enzymes from the extracted data set for further classification ...
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How to extract part of protein complex separated with HEADER with two molecules from one PDB file

I have a PDB file which contain two molecules (receptor and ligand). Each molecule will have its own header. All in ONE PDB file. ‌The header of receptor section looks like this (line 1-6 of the PDB ...
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Help me in understanding the PDB file

Can anybody please explain the below line to me. "We took the structure and coordinates of nogalamycin from the X-ray structure determined in PDB code = 1D17" What do I need to download from ...
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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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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 ...
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getting PDB file of interested sequence

I want a PDB file of DNA sequence I am interested in (10 base pairs) for docking. I will appreciate if any of you can please clarify some of my doubts. Do you think, I can generate PDB file by using ...
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How do you search for new enzymes that are more stable for handling, immobilization?

Noob here. I get that I should deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, ...
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Does the Protein Data Bank contain the estimated distances obtained using NMR spectroscopy?

From the Wikipedia entry on the Protein Data Bank (PDB) (emphasis mine): Most structures are determined by X-ray diffraction, but about 10% of structures are determined by protein NMR. When using X-...
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How can I calculate the distances between two specific residues of a protein from a PDB file?

Suppose, we have a protein (16PK). We are considering a 5-residue segment/window. If we assume ASN10 to be the ...
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Python script to simultaneously generate multiple pdbqt files for AutoDockTools?

I have a folder of pdb ligand structures that I'd like to test in some docking experiments with a certain protein using AutoDock Vina. I am not familiar with Python so I've always been using the ...
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programmatically select and label peptides within pdb file

I have a pdb file of a protein structure, and I would like to programmatically select certain peptides and label them in an annotated pdb file output, so that when the output pdb file is opened again ...
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How to show that one docking is better than another with Pymol visually

I have the following docking results: Dock_1 has better energy score than Dock_2. What I want to do is to show with Pymol that <...
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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'...
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Best way to dock subset of protein PDB and definition of a ligand

I have extracted residue 45 to 88 from a PDB file (2YRQ). With that I have a new smaller PDB file. Let's call it 45_88.pdb And I want to dock it to some other full protein. My question is what's the ...
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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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How to index residues by icode in biopython?

I am indexing a structure by the code below: ...
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4 answers
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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 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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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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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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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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6 votes
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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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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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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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