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
1answer
26 views

.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
1
vote
1answer
34 views

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)?
1
vote
2answers
79 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 ...
0
votes
0answers
18 views

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 ...
0
votes
1answer
49 views

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. ...
0
votes
2answers
37 views

.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 ...
0
votes
1answer
30 views

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 ...
1
vote
1answer
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 ...
1
vote
2answers
136 views

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 ...
1
vote
1answer
91 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 ???
0
votes
1answer
38 views

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 : ...
1
vote
1answer
89 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 ...
2
votes
3answers
42 views

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. ...
0
votes
0answers
12 views

How to rescore docked protein-ligand poses?

I have a set of several protein-ligand complexes in pdb format which I generated using Schrodinger software. I would like to rescore the whole set to obtain scoring results once again, given that I ...
1
vote
0answers
23 views

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 ...
1
vote
1answer
69 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 ...
0
votes
2answers
30 views

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 ...
0
votes
1answer
55 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: ...
0
votes
1answer
38 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.
1
vote
1answer
68 views

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 ...
3
votes
2answers
188 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
4
votes
3answers
76 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 ...
3
votes
1answer
93 views

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 ...
1
vote
1answer
55 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 ...
1
vote
0answers
20 views

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 ...
0
votes
1answer
78 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 ...
3
votes
0answers
34 views

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 ...
1
vote
1answer
84 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 ...
2
votes
2answers
276 views

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 ...
2
votes
1answer
148 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 ...
3
votes
1answer
111 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 ...
1
vote
0answers
34 views

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 ...
3
votes
1answer
64 views

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 ...
2
votes
1answer
149 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 ...
3
votes
1answer
63 views

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 ...
3
votes
1answer
53 views

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 ...
0
votes
1answer
40 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-...
4
votes
2answers
212 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 ...
4
votes
1answer
100 views

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 ...
2
votes
1answer
392 views

What are the differences between “Site” and “CONECT” in a PDB file

The CONECT section in a PDB file describes atomic connectivity. The SITE section describes (among other characteristics), ...
-2
votes
2answers
241 views

Web scraping in R

I have ~130 gene names of different human proteins. I'm looking for a convenient and systematic way to locate each gene's location in the genome, extract its CDS sequence and find whether there are ...
7
votes
2answers
880 views

Is there a standard way to clean a PDB file and re-number its residues?

Is there a pre-existing tool which will tidy up the numbering of a PDB file? Firstly, I would like to re-number the residues on inserts to make the icode an actual residue in the chain (by that I ...
2
votes
1answer
400 views

How to read the “SEQRES” section from a PDB file, using R

I'm using R and its Rpdb package to work with PDB files. I use the read.pdb function but, nevertheless, I couldn't find the argument which will allow me to view the ...
2
votes
1answer
18 views

What is the difference between the entity_src_genCategory tag and the entity_src_natCategory tag in pdb-xmls?

I want to read out the taxonomy id of the source organism of a pdb entry using the xml-file of the entry that is provided under ...
3
votes
2answers
152 views

How to find/build the evolutionary history of a protein from its sequence?

I aim to build the evolutionary history of a protein. For example given a FASTA entry how can I build an evolutionary tree? Here is the 5wxy protein for example: ...
3
votes
2answers
74 views

Is there a tool that can take a protein's amino acid sequence and would display it's locus on the genome?

I have the UNIPROT IDs, PDB IDs and FASTA files of several known proteins. I am looking for a tool that can take as input the protein's amino acid sequence and display the coding nucleotides of those ...
2
votes
1answer
457 views

getting KeyError on certain residues in BioPython: ATOM vs. HETATM lines

When I want to load atoms for residuum (' ', 85, ' ') in chain A for protein 3tmm with structure[0][chain_id][residue], but I'm ...
1
vote
0answers
12 views

“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 query, the ...
4
votes
2answers
122 views

Cross-reference with PDB database

I have a list of several thousand proteins and their UNIPROT IDs. I'm looking for an efficient method of cross-referencing it against the PDB tertiary structure database, and get a list of those ...
7
votes
2answers
374 views

How to get all PDB homologs from Uniprot (mapping + BLAST)?

I'd like to create a dataset consisting of all sequences which are either present in the PDB, or whose homolog is present in the PDB. In other words, any sequence in the PDB or any sequence related to ...