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Questions tagged [pdb]

Protein Data Bank, a publically available database of molecular structures of proteins

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16 votes
2 answers
487 views

Can two protein secondary structures "overlap" in the PDB?

I have a technical question regarding the syntax in Protein Data Bank files. In the protein with PDB# 1AE9 (pdb file), there are two lines in the .pdb file: ...
Douglas S. Stones's user avatar
8 votes
2 answers
840 views

How can I pare down a PDB file in Python to only include specific residues?

I'm trying to make a script that will take a MTZ file (reflections), convert it into a CCP4 map, then pare that map down to only encompass a desired area to cut down on the size of my PyMol session ...
Nick T's user avatar
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6 votes
4 answers
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Compressing structural information in PDB files

There seems to be a lot of redundancy in PDB files. These files can of course be compressed with general-purpose compression programs like gzip, but I can't help but imagine that these tools are ...
jqp's user avatar
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6 votes
1 answer
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What is "chain identifier" in PDB?

The PDB file format is explained here. My question is what "chain identifier" is exactly? What is the difference between two residues which have the same sequence number but different chain ...
Reza's user avatar
  • 275
6 votes
1 answer
217 views

How do I prepare a PDB for submission to the Protein Data Bank?

I have a couple structures that are nearly ready to be deposited in the PDB. Out of curiosity, I ran them through the ADIT's precheck tool and they failed with one error after another, as I lacked ...
Nick T's user avatar
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5 votes
3 answers
436 views

Protein structures given in PDB and SNP's

There are millions of proteins given in PDB, the sequence for which we can download in FASTA format. There are also hundreds of SNP's given in NCBI dbSNP. My question is whether the proteins in PDB ...
user avatar
5 votes
2 answers
557 views

How to obtain a list of proteins sorted by the ~1400 unique protein folds?

The databases CATH and SCOP both have around 1400 unique protein folds recorded from analysis of the PDB. However, I do not see any method to access this particular data. A list of each of the 1400 ...
Aalawlx's user avatar
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4 votes
2 answers
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How can I evaluate the hydrophobicity and/or surface charge of a protein?

How should I evaluate protein surfaces in terms of hydrophobicity and surface charge properties of the surface. Particularly I am looking to compare hydrophobic patches or surface charge between two ...
João Cardoso's user avatar
4 votes
2 answers
1k views

Proteins with alpha helices alone and beta sheets alone?

I would like to see some examples of proteins with PDB ID so that I can download and see them in VMD software. I need some proteins with alpha helix only and proteins with beta sheets alone.
dexterdev's user avatar
  • 1,133
4 votes
1 answer
121 views

Parse PDB using DSR-PDB Library

I'm trying to parse ATOM section of a PDB file. I'm using the dsr-pdb library for this purpose. I've encountered a problem. This library interprets CD1 atom of ILE ...
cartoonist's user avatar
3 votes
1 answer
1k views

Do residue sequence numbers in PDB files correspond to the positions in the backbone?

In other words if two residues have sequence numbers, say, 20 and 21 then are they next to each other in the backbone? If no (or not necessarily) then is there any way to find consecutive residues ...
Reza's user avatar
  • 275
3 votes
2 answers
121 views

Relationship between an Integrin-binding peptide and the Collagen type that it models

Recently, I have been investigating whether collagen can interact with integrin α2 (the product of human gene ITGA2). There is a structure in the protein data bank (...
Wan NIE's user avatar
  • 31
3 votes
1 answer
352 views

Why do chain identifiers in PDB have no standard starting chain id type?

At first I assumed that PDB chain identifiers are just uppercase letters (A, B, C,..) but found out there are protein chain ids that are numbers (0-9) and lowercase letters as well. For example, ...
Alpha Pacada's user avatar
3 votes
1 answer
501 views

Aligning two PDB structures with different numbers of atoms

What options do I have to align two PDB-files of ribosomes but with different number of atoms? I need to do the alignment using selection "name CA or name P", because the ribosome has both ...
HungryMolecule's user avatar
3 votes
0 answers
141 views

How to get a pdb file of a single atom?

I am trying to get a pdb file that contains a single atom, it doesn't matter if it's Hydrogen or another atom. How can I obtain this? Are there any pdb files with just a single atom available to ...
user4352158's user avatar
2 votes
2 answers
2k views

How to build a trimeric protein structure from monomeric PDB file?

Problem: I have a PDB file, with a monomer, but I would like to show the entire structure - which is trimeric - but I don't understand how to merge/build or combine the monomeric units to its full ...
CuriousTree's user avatar
2 votes
2 answers
3k views

MOL2 to PDBQT conversion via OpenBabel and MGLTools removes hydrogen atoms

I am trying to convert a MOL2 file (includes partial charges and hydrogen atoms) into a PDBQT file for re-scoring in AutoDock Vina. However, both approaches that I tried don't keep the hydrogen atoms ...
user avatar
2 votes
1 answer
158 views

How to edit manually pdb structures?

I would like to manually movement some b-sheets from a 3D structure of my PDF protein to represent a change in its structure.There some tool i can do that?
DaudAssassin's user avatar
2 votes
1 answer
1k views

Can pymol show cartoon (secondary structure) for a pdb of multiple frames?

I am using pymol to visualise the secondary structure of protein using its cartoon representation. The ...
lanselibai's user avatar
2 votes
1 answer
109 views

How to predict Protein-Protein Interactions from a pair of gene symbols?

I have a list of pairs of gene symbols who interact (putatively) and would like to assign each pair a score (and record other details) based on the predicted Protein-Protein Interaction (PPI). The ...
Joshua Garrison Burkhart's user avatar
2 votes
1 answer
79 views

How do I identify the carbonyl atoms in a PDB file

Can I infer it from the atom name alone? Or do I need to look at the structure of the residue it is in?
Ivan Spirandelli's user avatar
2 votes
0 answers
43 views

Can the protein extinction coefficient be calculated on a 3D structure pdb file?

I have so far only seen programs that work on monomeric amino acidic (1D) sequences, like ProtParam, but now that more 3D protein structure predictions can be trusted, I wonder if there is an ...
719016's user avatar
  • 1,790
1 vote
1 answer
67 views

How to filter out the antibody light chains into kappa and lambda types on the PDB website?

The antibody light chains can either be kappa or lambda types. I am searching homologous sequences on the RCSB PDB website. Is there a way to filter out these two types?
lanselibai's user avatar
1 vote
2 answers
276 views

PDB file for Osteopontin (SPP1)

I am looking for PDB file for Osteopontin (SPP1). The entry- 3CXD shows the structure of an Osteopontin antibody, not of the protein itself. Thanks
Mahdi's user avatar
  • 11
1 vote
1 answer
206 views

Transformation of coordinates found in PDB

According to the PDB guide there are some coordinate translation matrices found in PDB file: ...
Slowpoke's user avatar
  • 125
1 vote
1 answer
193 views

How many proteins on PDB have unknown function?

I was wondering how many of the files in the Protein Data Bank (PDB) have unknown function. The only paper I can find from an internet search is this one from 2012, which I assume might be outdated. I’...
João Areias's user avatar
1 vote
1 answer
95 views

PDB file SEQRES have different data?

In PDB file, SEQRES represent the aminoacids but some pdb file present the "GLC" and some other. for example ...
mkHun's user avatar
  • 149
1 vote
1 answer
134 views

How to conduct PSI-BLAST for a given protein sequence against bacterial protein database only?

I have a list of 100+ proteins and I need to conduct psi-blast for each one of them against "bacterial proteins" only. I went to NCBI's protein blast tool, but couldn't figure out how to select/limit ...
zhirzh's user avatar
  • 111
1 vote
2 answers
517 views

Counting the number of hydrogen bonds of multiple PDB files

I've been trying to figure out a systematic way to count the number of hydrogen bonds for multiple PDB files. DSSP shows me the total number of hydrogen bonds when I make ...
Daniel Bonetti's user avatar
1 vote
1 answer
180 views

How to parse SCOP parseable files PDB residue identifiers?

I am trying to parse the SCOP parseable files, specifically dir.des.scop.txt ver 1.75. But, I have been facing problems with the PDB residue identifiers in the file. This is a tab limited file and the ...
acharuva's user avatar
  • 113
1 vote
1 answer
276 views

How can I extract ligand with neighboring protein atoms from PDB with complex?

I'm not familiar with biology and coming from Data Science field, so please excuse me for the lack of knowledge. What I want is to create 3D voxel representation of ligand atoms with neighboring part ...
Slowpoke's user avatar
  • 125
1 vote
1 answer
77 views

how to reconcile PDB structures' sequences via Uniprot references?

I’m trying to reconcile structures in PDB entries with their sequences as reported in their chemList.polymer.dbref entries. E.g.: considering structures for HIV ...
rikb's user avatar
  • 123
1 vote
1 answer
403 views

How can I compare the STRIDE and DSSP output files of a particular pdb file?

I have the pdb file of H-ras protein 5P21.pdb. I am supposed to compare the output of DSSP and STRIDE files after feeding this pdb file to respective servers. My question is how to make a quick ...
dexterdev's user avatar
  • 1,133
1 vote
1 answer
71 views

Where can I find pdb files for macromolecules like receptors?

I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.
Josh Pinto's user avatar
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1 vote
0 answers
21 views

What is the oligomeric state of Leptospira LipL32 protein?

Does anyone know the oligomeric state of the mature and functional lipoprotein lipL32 in Leptospira? It's an outer membrane-bound protein. In its mature state, the signal peptide (residues 1-20) is ...
Anthony Nash's user avatar
1 vote
1 answer
439 views

How many different chains exist within a specific pdb file?

More specifically, if we want to understand the different chains within a protein, is it enough to look at the fourth column of all the lines that start with "ATOM" in a pdb file, and see how many ...
Yasmin 's user avatar
1 vote
0 answers
112 views

How can I perform a 1:1 sequence-structure alignment for a pdb template dimer and homologous dimer sequence?

I have: 1. A PDB dimer protein structure template of a real solved protein. 2. An unsolved, but highly homologous dimer protein (>90% sequence identity.) How can I use MODELLER to make a theoretical ...
Aalawlx's user avatar
  • 423
1 vote
0 answers
215 views

How does RCSB determine the origin of the Cartesian coordinate system utilized in all PDB files

When perusing through the text version of a PDB file, I noticed in records that begin with "ATOM," there are x, y, and z coordinates for these atoms. How is the origin of each molecule's Cartesian ...
HighEnergy's user avatar
1 vote
1 answer
72 views

Can one use DSSP (secondary structure assignment) for short peptides of size 6, 10 and 18?

I have large number of PDB files of peptides of size 6, 10 and 18. I wanted to cluster the peptide structure based on the secondary structure. I used DSSP in mdtraj module in python to assign DSSP ...
vigneshwaran kannan's user avatar
0 votes
1 answer
52 views

How is the "global pLDDT" score in the Protein Data Bank calculated?

Consider this list of entries for the Tobacco Mosaic Virus (TMV). I selected to sort by 'Global pLDDT' from best to worst. It is my understanding that pLDDT is usually calculated per residue for a ...
Ivan Spirandelli's user avatar
0 votes
1 answer
89 views

Structure coordinates in PDB file

How the atoms-residues-amino acids structure information prioritized? Specifically, I am trying to understand how the first atom is identified since it does not seem to correspond to the first amino ...
Stephen 's user avatar
0 votes
2 answers
87 views

How to find a PDB structure of a protease with a peptide like inhibitor

I wonder how, for purposes of just illustrating some concepts like substrate alignment in the catalytic triad active site, I can quickly and efficiently find a protease structure (irrelevant of what ...
TMOTTM's user avatar
  • 583
0 votes
0 answers
269 views

How to fix outliers in Ramachandran plot using Coot

I have the following Ramachandran plot generated by Coot: Notice that it has high outliers content (red dots). I want to manually drag those red dots into some part of the region. Eventually, I ...
littleworth's user avatar
0 votes
1 answer
148 views

How to convert PDB file of Amino Acids to rotamer tuples list of all AAs instances

Either by Python command, or via specific application (like Chimera) publicly available. Please provide example or link to one of. I have to detect AA location within MAP (density) 3D matrix. And to ...
Leon Kigelman's user avatar
0 votes
1 answer
316 views

Color van der waals bonds in swiss PdbViewer

I'm trying to color certain amino acid's van der waals bonds as in the following picture: can anybody please describe the steps to accomplish that?
Ranco's user avatar
  • 143