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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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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 ...
BioTL's user avatar
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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 $...
upontu's user avatar
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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 ...
LameSloth's user avatar
2 votes
2 answers
576 views

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 ...
Camps's user avatar
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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? ...
user18494's user avatar
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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 ...
Paul's user avatar
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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 ...
user366312's user avatar
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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 ...
user366312's user avatar
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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 ...
Irfan's user avatar
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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 ...
Priyanshu Gupta's user avatar
2 votes
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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 ...
vigneshwaran kannan's user avatar
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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 ...
vigneshwaran kannan's user avatar
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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, ...
Shafayet Rahat's user avatar
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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 ...
chengyun zhang's user avatar
3 votes
0 answers
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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?
raysas's user avatar
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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 ...
Harish Prabhakar's user avatar
3 votes
1 answer
318 views

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 ...
Spartan 117's user avatar
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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 ...
rtviii's user avatar
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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...
rtviii's user avatar
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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 ...
user366312's user avatar
2 votes
1 answer
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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 ...
maciejwww's user avatar
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4 answers
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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: ...
maciejwww's user avatar
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1 answer
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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(...
AlirezaBest's user avatar
3 votes
3 answers
476 views

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 ...
Dembappe's user avatar
1 vote
2 answers
70 views

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 ?
arinjoy datta's user avatar
1 vote
1 answer
51 views

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: ...
user366312's user avatar
2 votes
2 answers
96 views

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.
Jatin Kashyap's user avatar
1 vote
1 answer
137 views

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 ...
user366312's user avatar
2 votes
1 answer
66 views

Mapping PDB ID + chain ID to UniProt ID

This question was addressed here. Unfortunately, including bioservices, the solutions pypdb and ...
Johnny Tam's user avatar
7 votes
3 answers
2k views

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, ...
epsilone's user avatar
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1 vote
1 answer
300 views

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 ...
Ivo Palabra's user avatar
4 votes
1 answer
184 views

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)
user366312's user avatar
3 votes
2 answers
64 views

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 ...
user366312's user avatar
3 votes
1 answer
77 views

How can I parse alternative atom information?

I am trying to parse PDB files. Say, a PDB file has the following data: ...
user366312's user avatar
1 vote
1 answer
70 views

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 <...
user366312's user avatar
1 vote
0 answers
97 views

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 ...
user366312's user avatar
3 votes
1 answer
262 views

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 ...
drorhun's user avatar
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1 vote
1 answer
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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 ...
Husna Riyaz's user avatar
0 votes
1 answer
41 views

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. ...
amirre's user avatar
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1 vote
1 answer
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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 ...
user3001408's user avatar
2 votes
1 answer
56 views

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, ...
neversaint's user avatar
2 votes
0 answers
18 views

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 ...
microbeprincess's user avatar
6 votes
2 answers
251 views

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 ...
CubeHead's user avatar
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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 ...
이명훈's user avatar
1 vote
1 answer
435 views

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?
user366312's user avatar
3 votes
1 answer
151 views

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 ...
CubeHead's user avatar
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4 votes
1 answer
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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 ...
user366312's user avatar