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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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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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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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 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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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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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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Generating 3D cartesian coordinates of a peptide and computing van der Waal interactions (1-4 atoms) for a given set of dihedral angles?
I wanted to generate 3D Cartesian coordinates of a peptide sequence for fixed bond lengths and bond angles for a given set of backbone dihedral angles and side dihedral angles. I also wanted to ...
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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 ...
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Detect monomer from from multimer structure in PDB files?
I have a bunch of .pdb files that consist of protein-peptide structures. However, before start working with them I need to clean them. Now, I can easily remove water, ion, or other stuff like BMET, ...
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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 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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complete the res type in sdf
I use the diffdock (link to diffdock on github) to dock a peptide with protein and this tool give me a ligand in sdf file format. I traslate this ligand sdf format file to a pdb format file and find ...
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Molecular dynamic simulation, reconstuction of protonation pattern of a protein from PDB file without resolvent hydrogen
I'm trying to build a topology of a protein using GROMACS. The pdb file do not include coordinates of hydrogen atoms. So I was wondering how to assign appropriate protonation states for each residue. ...
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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:
...
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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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What tool(s) can I use to use a .faa file to feed into JSMol?
JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta ...
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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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Why do XRAY (but not CryoEM) structures of ribosome in PDB have 2 assemblies?
When i started programming against PDB i had a mixture of confusion & frustration with the fact that certain cif files contain two actual structures aka ...
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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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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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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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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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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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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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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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What is changed in this PDB file?
I used a tool called reduce to add Hydrogen bonds information to the PDB file.
I used the command:
$ ./reduce -NOFLIP 2GB1.pdb > 2GB1_with_H.pdb
The output file ...
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Why are conversion output SMARTS strings are not the same for different file types of the same structure?
I've just used Open Babel to convert .sdf and .mol2 files to SMARTS, and I'm a bit surprised the output can be different for the same structure. It's confusing me that one structure, one piece of ...
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CONECT doesnt include all the connections the 1vfl macro molecule have in a pdb file
I have a 1vfl macro molecule with 3000 atoms in it. When i open it in DC accelrys visualizer. It has much bonds. but when i open the pdb file it just have 8 connections. You can download the pdb here(...
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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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Extract single frame with MDAnalysis
How can I do to extract a single frame as a pdb file from a trajectory traj.xtc file, by using MDAnalysis?
I've got a universe
u=mda.Universe('confout.gro','traj.xtc')
Then I selected a residue by ...
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How can I get the coordinates of Hydrogen atoms attached to alpha-carbon?
I am trying to extract the hydrogen atoms attached to the Ca carbon in N no. of proteins. I would be needing the coordinates to calculate its centroid. How should I do it in python ?
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How can I clean a PDB file using VMD or NAMD?
I have 3884 PDB files generated by pd2_ca2main. PD2 CA2main is server for reconstructing the backbone of Calpha proteins using Gaussian mixture models.
All of these files have duplicate atoms or ...
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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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Why am I not being able to detect all the bonds in a residue?
Let us consider the first seven atoms of the protein 1CRN.pdb:
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What are all the proteins used to train Alphafold 2?
I want to identify the proteins used on AlphaFold2. The website says it was trained on PDB files from before April 30th 2018, and templates that are used are from no later than Feb 15 2021 (although ...
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Mapping PDB ID + chain ID to UniProt ID
This question was addressed here.
Unfortunately, including bioservices, the solutions pypdb 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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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 ...
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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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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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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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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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What do these characters mean in a PDB file?
The 33rd atom information in 3nir.pdb is written as follows:
ATOM 33 N ATHR A 2 4.935 -11.632 15.046 0.74 2.95 N
How should I interpret <...
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How can I calculate the radius of a residue?
I want to read a PDB file and display/render the atoms using a graphics engine.
If I consider each residue in the protein as a solid sphere, what would be the radius of the sphere?
How can I calculate ...
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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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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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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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"No records to view" error in the "Drug and Drug Target Mapping" PDB's search engine
I'm using the "Drug and Drug Target Mapping" search engine (http://www.rcsb.org/pdb/ligand/drugMapping.do).
I've noticed that there are some drugs (generic names) that if they appear in the ...
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