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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4 votes
3 answers
278 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(...
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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 ...
1 vote
0 answers
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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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-1 votes
1 answer
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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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0 votes
2 answers
128 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 ...
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1 vote
1 answer
32 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?
3 votes
3 answers
138 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
51 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
48 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: ...
4 votes
1 answer
360 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 ...
1 vote
1 answer
46 views

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. ...
2 votes
2 answers
82 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.
1 vote
1 answer
59 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 ...
0 votes
0 answers
59 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 ...
1 vote
1 answer
90 views

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 ...
0 votes
0 answers
16 views

What are all the proteins used to train Alphafold 2?

I want to identify the proteins used on AlphaFold2. The website says it was trained on PDB files from before April 30th 2018, and templates that are used are from no later than Feb 15 2021 (although ...
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2 votes
0 answers
90 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 ...
5 votes
3 answers
559 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 ...
1 vote
0 answers
35 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 ...
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7 votes
3 answers
572 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, ...
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1 vote
0 answers
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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 ...
3 votes
1 answer
93 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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30 views

How to create an Alchem configuration file for NamD simulation?

I am trying to use NamD for Alchem simulation for a bilayer system. I am using the script below as the configuration file, but after the minimization step, I am getting this error: "FATAL ERROR: ...
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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 ...
1 vote
0 answers
252 views

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 ...
0 votes
0 answers
18 views

Hamiltonian that fully describe the protein-lignin interaction

What is the Hamiltonian of protein-ligand interactions that fully describes the interaction with the inclusion of the quantum mechanical part?
3 votes
1 answer
554 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 ...
0 votes
2 answers
337 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 ...
1 vote
1 answer
53 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
1 answer
323 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 ...
2 votes
0 answers
172 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 ...
0 votes
0 answers
543 views

Unable to install OpenBabel

I am working on building a script that tests the binding affinity of protein-ligand pairs generated by our ML model as positive/negative binding annotations. One of the steps in doing so requires the ...
2 votes
1 answer
45 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, ...
5 votes
2 answers
137 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 ...
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2 votes
0 answers
33 views

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 ...
0 votes
1 answer
32 views

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 ...
5 votes
1 answer
168 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 ...
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0 votes
1 answer
32 views

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 ...
5 votes
1 answer
238 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 ...
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2 votes
0 answers
40 views

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 ...
3 votes
1 answer
65 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 ...
0 votes
0 answers
44 views

Chimera- How to go about changing the threshold of the EM map?

It is my first time using Chimera. I have uploaded a PDB file on to Chimera and opened it up on the software. I need to change the threshold of the EM map so that I can analyze what the EM map would ...
3 votes
1 answer
97 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 ...
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3 votes
1 answer
55 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 ...
5 votes
2 answers
170 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 ...
1 vote
0 answers
52 views

How to identify different protein domains using HHpred

I am new to HHpred/ analyzing proteins so bare with me. I have been given an uncharacterized protein, whose FASTA sequence I have obtained from Uniprot. I am looking to do the following by using ...
0 votes
1 answer
47 views

What does it mean by "PC" in this article?

What does it mean by "PC" in this article? a fast and efficient Cα-based method for accurately assigning protein secondary structure elements
2 votes
1 answer
137 views

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 ...
2 votes
2 answers
89 views

How to make MSA for contact prediction?

I'd like to try a contact prediction method (like TripletRes, CCMpred etc) using a custom set of sequences. There are about 1.5M sequences, all very similar to the canonical sequence; their ...
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0 votes
0 answers
76 views

Extracting and analyzing structure data of multiple proteins from PDB using Python

I am new to programming and I am given the task to extract structural data of soluble proteins from PDB and then shortlist the soluble enzymes from the extracted data set for further classification ...