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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Conversion of PDB to mmcif results in bond between the ligands getting broken
I am trying to convert a pdb file to mmcif file format. But the covalent linkages between the ligands are getting broken when I save it in mmcif format. Happens both in Chimerax and pdb_extract. Any ...
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How to interpret mutagenesis results from pymol to make conclusions about structural/functional changes and predict resulting pathogenesis?
I'm a beginner bioinformatics student. I am currently working on my first project. We have gathered data about SNPs that are associated with a particular disease. We aim to understand the functional ...
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How can I visualize protein secondary structure?
I'm currently working on a secondary structure prediction model and I'd like to visualize what will be predicted , the format of secondary structure sequence is consisted of 8 labels:
G: 3-turn helix ...
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LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI
I am trying to determine the interaction of the targeted amino acid with other amino acids, but I am having trouble. When I pass a PDB file of a protein that has ligands, I can see the interactions. ...
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Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank
Is there a way to download all data containing amino acid sequence - secondary protein structure from protein data bank(https://www.rcsb.org/).
Or is there a way to extract the data programaticaly ...
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Low confidence score from alphafold2_multimer_v3
I am running alphafold2_multimer_v3 in ColabPro (A100 40 GB GPU) with the following parameters:
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Is there any standardized and ready-to-use dataset available online for download regarding protein geometry? [closed]
I want to do ML model training and data analysis for secondary structure prediction.
Is there any standardized and ready-to-use dataset available online regarding protein geometry?
For example, the ...
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How can I detect secondary structures in a protein using a hydrogen bond detection algorithm?
Suppose I have a protein chain. And I have a hydrogen bond detection algorithm that can detect hydrogen bonds in a protein chain. Say, the name of the algorithm is HBDA algorithm.
How can I detect ...
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How to create a dataset of contact maps of homologous proteins?
Disclaimer: I am a machine learning researcher working on network science and want to use proteins to test an algorithm of mine using real-world data. My bioinformatics knowledge is minimal.
I need to ...
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Method for reproducing minimal, cartoon-style protein structure visualisation
I recently came across a preprint ( DOI, PDF link ) that has some figures of protein structures in a style that I have not seen before. To me it appears easier on the eyes and less noisy than the ...
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Protein symmetry classification from PDB data
Given the PDB or mmCIF information of a homomeric protein assembly whose global symmetry is unknown, how might one design an algorithm to find which point group symmetry class it belongs to (cyclic $...
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Tools and software to visualize the moving cell compartments in 3D
Also asked on biostars
I am looking for tools and software that could help me visualize moving cell compartments in 3D where I can go from the cell membrane to the ER, then out with the protein into ...
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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 ...
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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 ...
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Best Library for 3D Protein Structure Visualization and Annotation
I have a background in Computer Science and have recently gotten very interested in the field of Protein Engineering. I am trying to build a web app which displays the 3D structure of a protein when I ...
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Energy error margin for protein structures
I would like to know the acceptable error margin for the lowest free energy of a protein. In other words, say, both Group A and B have determined the lowest free energy of the same protein in their ...
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Does AlphaFold actually calculate the fold?
After reading through papers and the code, I'm still not clear if AlphaFold and the like do actually calculate the 3D structure. My current feeling is that they are more like information retrieval ...
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Downloading a list of all RCSB-PDB entries
I'm trying to download a list of all of the non-redundant protein chain IDs in the RSCB-PDB (not the actual FASTA entries, just the IDs), filtered by some % identity.
Does anyone know how to do this? ...
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Old program make error ProtDeform
Im trying to run ProtDeform on ubuntu 20.04
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125161/
I need scoring function :/ to my project
But error occurs:
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Finding mutations in glycosylation sites
We are going to look at the likely N- and O- glycosylation sites within MUC16 (Q8WXI7 · MUC16_HUMAN)§ by in house long-read DNA sequencing data (PacBio).
Counting the number of tandem repeats is a ...
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How do I delete an amino acid residue from a loop and then join the loose ends?
I want to delete an amino acid residue from a loop and then join the loose ends. I intend to increase the thermal stability of the protein by reducing the size of the loop and its agitation. Pymol ...
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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 ...
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Is there any python module to assign secondary structures which includes both Polyprolene region as well as individual strand as well?
I wanted to assign secondary structure to set of pdb files. However, DSSP and STRIDE cannot assign for single peptides if it is falling inside single long beta strand or polyprolene region as it does ...
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Generating 3D cartesian coordinates of a peptide and computing van der Waal interactions (1-4 atoms) for a given set of dihedral angles?
I wanted to generate 3D Cartesian coordinates of a peptide sequence for fixed bond lengths and bond angles for a given set of backbone dihedral angles and side dihedral angles. I also wanted to ...
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Protein fold topology search web-server
I'm finding a web server (or standalone program) that allows the upload of a custom PDB for protein fold topology search.
Do you know any of them?
More details:
Actually I started off with Foldseek ...
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Detect monomer from from multimer structure in PDB files?
I have a bunch of .pdb files that consist of protein-peptide structures. However, before start working with them I need to clean them. Now, I can easily remove water, ion, or other stuff like BMET, ...
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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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What tool(s) can I use to use a .faa file to feed into JSMol?
JSMol, the molecular modelling software, requires PDB file format to work and render the graphics. Currently, I am writing an annotation software - backend in Perl - that takes in a .faa file (fasta ...
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Why do XRAY (but not CryoEM) structures of ribosome in PDB have 2 assemblies?
When i started programming against PDB i had a mixture of confusion & frustration with the fact that certain cif files contain two actual structures aka ...
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computing the distance between ( XYZ coordinates)
I have a txt file (50k) proteins in it, which looks like this:
line 1:the protein code
line 2: protein length in amino acids
line 3: amino acid sequence
line 4: secondary structure
line 5: XYZ ...
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open and read Fasta file (raw data)
I have a big fasta.dataset file containing half a million proteins (1.0 GB). I have four lines for each protein code:
line 1:the protein code
line 2: protein ...
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How can I predict the folding of a synthetic protein?
I want to predict the folding of a chimeric antigen receptor sequence. These sequences are completely made out of small parts of different proteins. Do you know if AlphaFold can be used for this?
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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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How can I get the coordinates of Hydrogen atoms attached to alpha-carbon?
I am trying to extract the hydrogen atoms attached to the Ca carbon in N no. of proteins. I would be needing the coordinates to calculate its centroid. How should I do it in python ?
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Why am I not being able to detect all the bonds in a residue?
Let us consider the first seven atoms of the protein 1CRN.pdb:
...
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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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What options should I explore to improve the output of the protein reconstruction?
We developed a neural network-based protein reconstruction tool to reconstruct the main chain from only CA atoms.
we generated data from some selected PDBs from the RCSB website to train an NN model.
...
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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.
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How can I clean a PDB file using VMD or NAMD?
I have 3884 PDB files generated by pd2_ca2main. PD2 CA2main is server for reconstructing the backbone of Calpha proteins using Gaussian mixture models.
All of these files have duplicate atoms or ...
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What does it mean by a Local Coordinate in the case of protein chains?
High-performance transformation of protein structure representation from internal to Cartesian coordinates
In Figure 3a, each residue has its own local coordinates, which are illustrated shown using ...
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When does a 2D histogram / heatmap take a circular shape?
The above is a 2D histogram of y and z internal coordinates describing the positions of C-alpha atoms involved in hydrogen bonds between antiparallel Beta-strands.
There is no color coding. It is ...
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Writing to .cif from BioPandas
My question is twofold. First, I've run into an issue working with .cif files and pandas dataframes. With BioPandas, I can read a .pdb file into a dataframe and then go the opposite direction, writing ...
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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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How can I measure the distance between each pair of carbon alphas in overlayed protein structures?
I am trying to make a figure in which the protein structures are colored by the distance between the calphas in the overlayed structures.
I am comparing our cryoEM structure to that of a previous ...
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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 can I calculate the radius of a residue?
I want to read a PDB file and display/render the atoms using a graphics engine.
If I consider each residue in the protein as a solid sphere, what would be the radius of the sphere?
How can I calculate ...
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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 to identify most important Amino Acid residues in a given protein?
Continuing from the title, in my context, important means that changing the set of AAs (either or one more many) changes the domain and/or fold and/or function and/or family etc.
I noticed that there ...
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Installation of Biovia DS visualiser on ubuntu
I am trying to install Biovia DS visualiser2021 on ubuntu 22.04. I used the procedure from the following website
https://askubuntu.com/questions/1175772/cant-install-discovery-studio-visualizer
When I ...
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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 ...
