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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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 ...
Katherine's user avatar
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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 ...
Omar Shehab's user avatar
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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. ...
biocodz's user avatar
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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? ...
user18494's user avatar
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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 ...
Aureo André Karolczak's user avatar
3 votes
2 answers
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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 ...
user366312's user avatar
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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 ...
vigneshwaran kannan's user avatar
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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 ...
vigneshwaran kannan's user avatar
2 votes
1 answer
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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 ...
Johnny Tam's user avatar
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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, ...
Shafayet Rahat's user avatar
4 votes
3 answers
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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(...
Amal's user avatar
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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 ...
Harish Prabhakar's user avatar
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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 ...
Amal's user avatar
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2 answers
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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 ...
Amal's user avatar
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1 answer
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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?
AntimatterNebula's user avatar
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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 ...
Dembappe's user avatar
1 vote
2 answers
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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 ?
arinjoy datta's user avatar
1 vote
1 answer
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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: ...
user366312's user avatar
4 votes
1 answer
379 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
1 vote
1 answer
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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. ...
user366312's user avatar
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.
Jatin Kashyap's user avatar
1 vote
1 answer
113 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 ...
user366312's user avatar
1 vote
1 answer
102 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 ...
user366312's user avatar
1 vote
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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 ...
user366312's user avatar
2 votes
0 answers
167 views

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 ...
Brookspj's user avatar
5 votes
3 answers
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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 ...
jambajuice's user avatar
1 vote
1 answer
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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 ...
Logan's user avatar
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7 votes
3 answers
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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, ...
epsilone's user avatar
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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 ...
user366312's user avatar
3 votes
1 answer
197 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 ...
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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 ...
bababee's user avatar
1 vote
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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 ...
user15571's user avatar
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
0 votes
2 answers
752 views

Pymol: select low confidence regions from AlphaFold pdb file

I have downloaded a predicted structure from AlphaFold as a pdb file (https://alphafold.com/entry/O75376) and loaded it into Pymol (2.3.0). There is quite a large portion of the structure that was ...
justinian482's user avatar
1 vote
1 answer
71 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 ...
user3001408's user avatar
2 votes
1 answer
616 views

What is the different between the I-TASSER, phyre2, SWISS-model in the 3D tertiary structure?

What is the difference between the I-TASSER, phyre2, and SWISS-model in the 3D tertiary structure? How do they get the results? When I did a prediction, I got a similar result for the highest template ...
Sewar Khassawneh's user avatar
3 votes
1 answer
495 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
2 votes
1 answer
54 views

How reliable is Alphafold2 for folding random-coil peptide

I have a peptide X of length 50aa. Alphafold2 predicted the structure which takes a helix form and with high average pLDDT score (>90). But during actual experiment (e.g. crystallography, ...
neversaint's user avatar
5 votes
2 answers
233 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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What is coarse-grained modeling of proteins?

I need beginner-level study materials for coarse-grained modeling of proteins. Can anyone supply me with entry level resources besides the Wikipedia article? Background Coarse grain protein modelling ...
user366312's user avatar
0 votes
1 answer
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How can I draw a diagram of hydrogen bonds only on the basis of C-alpha backbone?

We are working on an algorithm to assign proteins only on the basis of alpha-carbons. My teacher told me to draw a diagram to represent hydrogen bonds only on the basis of alpha-carbons. I showed him ...
user366312's user avatar
6 votes
2 answers
237 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
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0 votes
1 answer
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How to represent a summary of disagreement between two secondary structure predictors given predictions for many proteins?

I have 6000 predicted protein structures. I am comparing secondary structures predicted by an algorithm with the correct secondary structure assignments. I need to show which positions in a predicted ...
user366312's user avatar
5 votes
1 answer
397 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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2 votes
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Secondary structure assignment tool

Is there any CA-based online tool/web-server available for secondary structure assignment of proteins except DSSP or STRIDE? DSSP is a database of secondary structure assignments (and much more) for ...
user366312's user avatar