Questions tagged [pdb]
Protein Data Bank, a publically available database of molecular structures of proteins
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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 ...
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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 (...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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Transformation of coordinates found in PDB
According to the PDB guide there are some coordinate translation matrices found in PDB file:
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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 ...
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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?
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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,
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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’...
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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?
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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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.
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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
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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 ...
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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 ...
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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 ...
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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?
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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
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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 ...
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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.
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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 ...
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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:
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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 ...
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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 ...
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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 ...
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