Questions tagged [protein-structure]
The 3-D structure of a protein in space. It can refer to secondary structures, such as alpha helices or beta sheets, or the 3-D coordinates of the atoms making up a protein.
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How to select high quality structures from the Protein Data Bank?
Models of structures deposited in the Protein Data Bank vary in the quality, depending both on the data quality and expertise and patience of the person who built the model. Is there a well-accepted ...
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How can we find the distance between all residues in a PDB file?
If we have a PDB structrure, how can we find residues physically interacting with each other in space? I know that we must find the distance between residues and if the distance is less than 5-6 ...
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Chimera Alignments
I have a structure with two subunits. I am trying to show movement of the C-terminal subunit upon ligand binding by superposition with another structure from the same strain in the apo form.
I want ...
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Getting structure and sequence related to PDB IDs
I have two kinds of interactions: transient and stable. We are supposed to work on stable interaction, like interactions between two monomers in a heterodimer.
In a heterodimer there are two chains ...
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Phyre2 vs ITasser, completely different models generated
Does anyone have experience generating pdb structures with Phyre and ITasser online tools. The results generated from each given the same amino acid sequence input are very different and I am ...
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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 ...
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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, ...
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how to find the bound form of an enzyme structure?
For my undergraduate research I'm looking for a database that gives the bound form of a particular protein structure. Is there any database that provide us with such data? So far I've found following ...
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Minimizing particle-flow grid mapping time of a protein surface using spherical-coordinates and differentiation encoding [closed]
This is an interesting problem - I was wondering if anyone has a creative solution.
So I have a vector of vertices representing atoms in a protein, as well as 6 variables containing the absolute ...
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Do any publicly available databases detail protein structure and functional domains?
I am interested in finding a database that takes a gene or protein name as input (possibly with the option to specify transcript) and gives information about the protein's functional domains in terms ...
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Tool for predicting interactions in the cell
What tools are available to predict, based on the structure of a certain protein, its interactions within a cell?
For example, I am considering the split GFP protein and I am trying to predict if ...
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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 ...
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Why is it necessary to add hydrogen and delete water before protein-ligand docking?
What is the reason for adding hydrogen and removing unnecessary water molecules from the protein structure before protein-ligand docking? FYI, the tools I used for docking is GOLD.
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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 ...
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Why can't AlphaFold predict the consequences of point-mutations?
In the literature, it specifically states that AlphaFold has "Has not been trained to predict structural consequences of point mutations". See : https://alphafold.com/faq
AlphaFold has not ...
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Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles
I have been successfully using BioPython's functionality for extracting protein torsion angles using the IC_Chain module. However, I am currently looking to use the ...
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Identify side chain atoms in BioPandas dataframe
I am currently implementing some metrics I could use for comparing two conformations of the same protein in Python.
For example, I know I could use the RMSD of all protein ATOMS in BioPandas using ...
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How do I build a glycosylated protein from PDB files manually?
I have a large protein PDB file (~3500 residues) and a couple of PDB files containing glycan structures I sourced from GLYCAM.
How can I attach the N and O-glycans onto each protein residue with ...
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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 ...
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Differences between TM and GDT-TS scores for structure comparison [closed]
What are the relative advantages / disadvantages of the TM (template modelling) and GDT (global distance test, total score) scores, used in protein structure prediction competitions, such as CASP? ...
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Database for proteome-wide predictions of protein structures
Accuracies of protein structure predictors have improved quite a lot in recent years. Algorithms such as Rosetta have gotten robust enough to predict structures of large number of proteins. However, I ...
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Best distance parameter for estimating physical interaction between residues in a PDB file
We can calculate the distance between residues in a PDB file regarding different parameters like closest atoms, alpha carbon, beta carbon, centroid and etc. Which one of these parameters are better to ...
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How to retrieve sequences from a txt file by protein names from other txt file?
My problem is that I want to retrieve the sequences line + secondary structure line that match the protein names from the header.txt file:
The text file(...
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Why do we need to find minimum energy in a protein chain?
High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models
The above research paper is about a software tool for reconstructing a protein's main chain model only ...
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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 ...
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CCP4 file to a Python 3 numpy array or similar workaround
I would like to merge together several ccp4 formatted density maps (and do a few minor things).
So ideally I would like to open the ccp4/mrc files as numpy arrays in Python 3 and save the array as a ...
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How to quickly and robustly convert between mmCIF and PDB?
There is already a question on PDB/CIF to MMTF, however what is a robust way to programmatically go between PDB and CIF files?
For example I can use a python script from this gist that relies on ...
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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 ...
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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 ...
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What is protein secondary structure assignment?
I am absolutely new to Structural Bioinformatics (I only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using ML.
When it comes ...
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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
...
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How are tertiary protein structures represented in computers?
What data structure is used in representing protein structures in computers so that we can apply algorithms?
Matrix or Graph or tree?
P.S. I am absolutely new to Bioinformatics.
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What is DSSP algorithm for?
DSSP - Wikipedia
The above article says that DSSP is a hydrogen bond estimation algorithm. Then the article also says that this algorithm is "assigns secondary structure to proteins".
If ...
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Why is there a chloride ion in this 3D model?
Here we have a 3D model of a sequence that match with this sequence
VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK
in Blast
the 3D structure is here
Why is there a chloride ion in this 3D model?
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Putting labels of different sizes on one PyMOl Object
I'm new to PyMol (and StackExchange!) and working on my first project. I have the structure of a protein as an object, called PolyA-M, and the idea is that the residues of it are shown as spheres of ...
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Proteins with one SS bond?
I would like to find proteins with exactly one SS bond. Is there a database where I can search this? I've tried advanced search on https://www.rcsb.org/, but no such option, at least I could not find ...
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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 ...
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Folded Protein Chunk Dimensional Classification?
Are there known dimensional measurements for the classification of folded proteins given a starting chunk/domain as defined by something like the clustering functionality of MSM Builder?
Examples of ...
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Perform protein structure-based sequence alignment in Python
I am looking for a Python package that performs pairwise structural alignment of protein structures (i.e., PDB files) and returns a sequence alignment. PyMOL is able to do this through the GUI, for ...
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How to visualize electron density of a specific part of the protein residue?
Hi everyone (mostly who are interested in structural bioinformatics).
I face the problem that I cannot plot the electron density of a specific part of my protein. For the whole protein it is not a ...
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Programmatically adding hydrogen and remove water to multiple PDB files
I'm trying to dock a ligand to several hundred PDB files (receptors).
I thus need to prepare the those PDB files like removing water and adding hydrogen.
I can do that manually using Autodock or Pymol....
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How do you calculate the top L/5 score?
I am currently investigating how to predict protein structure and contact map predictions. There, I see things like top L/5 and top L/2 scores as a way to evaluate the contact map. What formulas do ...
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How many models should be generated by rosetta for denovo protein structure prediction?
How many models should be generated by rosetta for de novo protein structure prediction of a 382 long sequence? In the tutorial, it says 50,000 models but practically it takes a lot of time (weeks) to ...
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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 ...
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Protein fold pathfinding?
This is probably a long-shot since it would be so dependent upon the underlying folding algorithms. Are there known algorithms for mapping the path followed in a protein folding simulation when you ...
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Can VMD change its cartoon representation for secondary structure according to trajectories? [closed]
I am using VMD to visualise the secondary structure of protein here.
The trajectories are from my Gromacs simulation. Firstly I use ...
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How to extract subset of protein structure (PDB format) file based on a subsequence of that protein
I looking at a particular protein structure called 2LY4 accessible from RSCB PDB website.
The corresponding fasta sequence for that structure is this:
...
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Generate ligands candidates based on protein shape
Recent approaches to novel drug design using machine learning (ML) and deep learning, often involve generating hundreds of potential ligands which are later tested by docking with a target protein and ...
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What tool RCSB and AlphaFold use to visualize 3D structures?
I would like to implement on a web page a tool to visualize 3D structures like it is for AlphaFold and RCSB.
A couple of examples:
https://www.rcsb.org/3d-view/7KX9
https://alphafold.com/entry/Q5VSL9
...
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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.
