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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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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 ...
1 vote
1 answer
39 views

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 ...
1 vote
1 answer
45 views

Low confidence score from alphafold2_multimer_v3

I am running alphafold2_multimer_v3 in ColabPro (A100 40 GB GPU) with the following parameters: ...
2 votes
1 answer
38 views

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 ...
0 votes
1 answer
62 views

Does AlphaFold actually calculates the fold?

After reading through papers and the code, I'm still not clear if AlphaFold and the likes do actually calculate the 3d structure. My current feeling they are more like information retrieval engines. ...
1 vote
1 answer
83 views

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 ...
2 votes
0 answers
40 views

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 ...
2 votes
0 answers
33 views

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 ...
0 votes
0 answers
29 views

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 $...
0 votes
0 answers
16 views

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 ...
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 ...
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 ...
0 votes
0 answers
28 views

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 ...
1 vote
0 answers
59 views

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 ...
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 ...
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 ...
1 vote
1 answer
78 views

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? ...
1 vote
1 answer
94 views

Post docking evaluation

What to do after protein-ligand docking? Is there any necessary or enhancement step recommended after docking to validate the confirmation of highest score is the best? For your information, I am ...
1 vote
3 answers
593 views

How can I programmatically add a Hydrogen 'Atom' to a 'Residue' object?

I know the algorithm for creating a Hydrogen atom and adding to a residue: ...
0 votes
0 answers
79 views

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: ...
1 vote
0 answers
37 views

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 ...
1 vote
2 answers
301 views

Permutations of 4 amino acid sequence oligopeptide

I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon. I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
3 votes
1 answer
705 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 ...
1 vote
1 answer
108 views

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 ...
0 votes
1 answer
298 views

How to use multiple .pdb files as templates for homology modelling?

I just ran an AlphaFold job for PduK from the Pdu BMC operon and got very strange results including a large circular loop of random coil. According to Mayer et al., PduK should be semi-triangular ...
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 ...
1 vote
1 answer
61 views

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 ...
2 votes
1 answer
49 views

Differentiating molecules based on peptide sequence? How to annotate?

I want to differentiate between classical class I and non classical class I MHC molecules in a model organism using well conserved structural features within classical MHC I molecules (eg intradomain ...
2 votes
0 answers
16 views

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 ...
2 votes
1 answer
52 views

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 ...
1 vote
0 answers
68 views

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, ...
1 vote
1 answer
526 views

How to calculate RMSD and binding energy from the already docked ligand-receptor

I have the following PDB file that looks like this. It is downloadable here. This PDB already contains ligand and receptor together. The red molecule is the ligand and the yellow is the receptor. They'...
1 vote
1 answer
106 views

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 ...
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 ...
0 votes
0 answers
43 views

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 ...
4 votes
3 answers
327 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(...
1 vote
0 answers
50 views

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 ...
-1 votes
1 answer
137 views

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 ...
0 votes
2 answers
364 views

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 ...
1 vote
1 answer
59 views

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?
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, ...
0 votes
1 answer
221 views

How can I get a list of neighboring Hydrogen atoms of an alpha-carbon?

Suppose, I want to find the neighboring Hydrogen atoms of a specific C-alpha atom. The following was my effort. However, it produces a bunch of empty lists. ...
5 votes
2 answers
253 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 ...
1 vote
1 answer
92 views

Protein-Ligand in PDB

I am a newbie in bioinformatics. In PDB, while searching for proteins, I sometimes get protein with ligand, such as PDB ID 1J1Z. In cases I get pure protein structure, in some cases I get protein-with ...
2 votes
2 answers
96 views

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.
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 ...
1 vote
2 answers
70 views

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 ?
1 vote
1 answer
137 views

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 ...
3 votes
1 answer
269 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 ...
1 vote
1 answer
51 views

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: ...