Skip to main content

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.

Filter by
Sorted by
Tagged with
0 votes
1 answer
69 views

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-...
2 votes
1 answer
15 views

How can I search globular proteins by residue count in the RCSB databse?

I want to find some globular proteins with some of the longest individual chains that have all three types of secondary structures,, namely helix, sheet, and loop. So, I tried the following search: ...
2 votes
2 answers
50 views

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 ...
1 vote
1 answer
132 views

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 ...
3 votes
2 answers
884 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
2 votes
1 answer
86 views

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 ...
1 vote
1 answer
66 views

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 ...
0 votes
0 answers
29 views

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 $...
2 votes
1 answer
89 views

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 ...
1 vote
0 answers
249 views

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 ...
2 votes
2 answers
588 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 ...
2 votes
0 answers
27 views

(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 ...
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 ...
6 votes
3 answers
745 views

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 ...
1 vote
1 answer
77 views

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? ...
2 votes
3 answers
801 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 ...
0 votes
0 answers
16 views

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 ...
1 vote
0 answers
126 views

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 ...
0 votes
0 answers
27 views

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 ...
1 vote
1 answer
38 views

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, ...
0 votes
0 answers
55 views

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 ...
1 vote
1 answer
60 views

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 ...
2 votes
0 answers
16 views

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 ...
1 vote
0 answers
68 views

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, ...
3 votes
2 answers
354 views

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: ...
1 vote
1 answer
525 views

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'...
0 votes
1 answer
225 views

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 ...
2 votes
4 answers
919 views

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: ...
3 votes
0 answers
23 views

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?
0 votes
0 answers
43 views

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 ...
3 votes
1 answer
320 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 ...
1 vote
0 answers
50 views

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 ...
3 votes
2 answers
111 views

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...
0 votes
1 answer
42 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. ...
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, ...
3 votes
3 answers
183 views

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 ...
2 votes
2 answers
559 views

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 ...
1 vote
1 answer
92 views

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 ...
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.
1 vote
1 answer
41 views

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 ...
2 votes
1 answer
42 views

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 ...
1 vote
1 answer
21 views

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(...
3 votes
3 answers
478 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 ...
1 vote
1 answer
301 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 ...
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 ?
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 ...
3 votes
1 answer
266 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 ...
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: ...
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 ...
5 votes
4 answers
3k views

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 ...