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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 ...
marcin's user avatar
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10 votes
5 answers
11k views

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 ...
Sara's user avatar
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9 votes
2 answers
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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 ...
TW93's user avatar
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9 votes
1 answer
236 views

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 ...
Amanda Constantinides's user avatar
8 votes
2 answers
263 views

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 ...
Sara's user avatar
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8 votes
2 answers
963 views

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 ...
Te-Yo's user avatar
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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, ...
epsilone's user avatar
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7 votes
2 answers
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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 ...
Loch23's user avatar
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7 votes
0 answers
69 views

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 ...
Noga Aharony's user avatar
6 votes
3 answers
748 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 ...
The Sauralph's user avatar
6 votes
3 answers
97 views

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 ...
Dan's user avatar
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6 votes
3 answers
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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.
Zheng Keong Ng's user avatar
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 ...
CubeHead's user avatar
  • 425
5 votes
2 answers
254 views

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 ...
jaslibra's user avatar
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5 votes
3 answers
2k views

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 ...
Sara's user avatar
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5 votes
3 answers
2k views

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 ...
jambajuice's user avatar
5 votes
2 answers
251 views

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 ...
CubeHead's user avatar
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5 votes
1 answer
464 views

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 ...
CubeHead's user avatar
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5 votes
2 answers
543 views

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 ...
Quantumerical's user avatar
5 votes
0 answers
87 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 ...
James's user avatar
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5 votes
0 answers
259 views

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? ...
GingerBadger's user avatar
4 votes
4 answers
188 views

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 ...
user345394's user avatar
4 votes
3 answers
326 views

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(...
Amal's user avatar
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4 votes
1 answer
392 views

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 ...
user366312's user avatar
4 votes
1 answer
3k views

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 ...
James's user avatar
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4 votes
3 answers
101 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 ...
Jake B.'s user avatar
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4 votes
1 answer
639 views

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 ...
Matteo Ferla's user avatar
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4 votes
2 answers
178 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 ...
Adrian Smith's user avatar
3 votes
3 answers
479 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 ...
Dembappe's user avatar
3 votes
2 answers
251 views

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 ...
user366312's user avatar
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 ...
drorhun's user avatar
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3 votes
2 answers
53 views

Algorithm for counting neighbors

I need an algorithm to process protein chains. The volume size would probably not exceed 30x30x30 angstrom^3. Say, I have a point cloud of 50,000 points in a 3D space. I want to count the number of ...
user366312's user avatar
3 votes
1 answer
78 views

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.
user366312's user avatar
3 votes
1 answer
107 views

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 ...
user366312's user avatar
3 votes
1 answer
1k views

How to introduce point mutations in a protein structure?

I want to introduce point mutations to a protein PDB file and automatically predict the 3D coordinates of a new amino acid residue in the mutated protein. I used interactive Schrodinger's Maestro tool ...
Nurlybek Amangeldiuly's user avatar
3 votes
1 answer
62 views

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?
Dare to ask-I dnt mind punishm's user avatar
3 votes
2 answers
1k views

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 ...
A. King's user avatar
  • 41
3 votes
1 answer
54 views

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 ...
Jake B.'s user avatar
  • 205
3 votes
1 answer
122 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 ...
Jonathon Byrd's user avatar
3 votes
1 answer
46 views

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 ...
CoryG's user avatar
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3 votes
1 answer
1k views

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 ...
Francho Nerín Fonz's user avatar
3 votes
1 answer
699 views

How to convert Foldseek .m8 alignment files to FASTA format?

I want to use sequence alignments found by Foldseek in PROSS. I know there are other ways to get alignments (also tried with results of HHPred), but I had in mind that Foldseek may find remote ...
O.Laprevote's user avatar
3 votes
1 answer
107 views

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 ...
kitsune_breeze's user avatar
3 votes
1 answer
780 views

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....
littleworth's user avatar
3 votes
1 answer
589 views

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 ...
musako's user avatar
  • 195
3 votes
1 answer
106 views

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 ...
DanielSebas's user avatar
3 votes
1 answer
151 views

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 ...
CubeHead's user avatar
  • 425
3 votes
2 answers
61 views

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 ...
CoryG's user avatar
  • 195
3 votes
0 answers
36 views

Oligomer status prediction with Alphafold 2

I am new to using Alphafold 2 and have been primarily using ChimeraX and Colabfold to run some preliminary predictions. I am particularly interested in using AF2 to predict the homo-oligomerization ...
user48660's user avatar
3 votes
0 answers
22 views

Q8 Accuracy Evaluation metric mathematical expression used in Protein Secondary Structure Prediction

I am working on Protein Secondary Structure Prediction using Recurrent Neural Network (GRU) model. I came across few open source projects which already worked on the similar problem. All of them are ...
Muhammad Usman's user avatar