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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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
357 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 ...
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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. ...
1 vote
2 answers
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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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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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1 answer
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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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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
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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 ...
4 votes
3 answers
293 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 ...
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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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6 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, ...
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1 vote
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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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1 answer
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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 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
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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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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
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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 ...
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2 answers
193 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 ...
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1 answer
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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
229 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
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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 ...
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393 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
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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
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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
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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 ...
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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 ...
5 votes
1 answer
135 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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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
179 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
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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 ...
3 votes
1 answer
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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 ...
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0 answers
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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
87 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
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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
122 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
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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
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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
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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
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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
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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 ...
2 votes
1 answer
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Chou-Fasman Method Overlapping Regions Problem - Secondary Structure Prediction

According to the Chou-Fasman method, when there is an overlapping region on the amino acid sequence, we compare the scores of alpha-helix and beta-sheet and chose the highest one. Let's say I have ...
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0 votes
1 answer
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How to extract part of protein complex separated with HEADER with two molecules from one PDB file

I have a PDB file which contain two molecules (receptor and ligand). Each molecule will have its own header. All in ONE PDB file. ‌The header of receptor section looks like this (line 1-6 of the PDB ...
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1 answer
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Help me in understanding the PDB file

Can anybody please explain the below line to me. "We took the structure and coordinates of nogalamycin from the X-ray structure determined in PDB code = 1D17" What do I need to download from ...
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2 answers
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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 ...
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1 vote
2 answers
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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: ...
1 vote
1 answer
232 views

How to show electrostatic interactions in Pymol on the wanted residue

I have the following Pymol visual, The green molecule is receptor and red/yellow is the ligand. In the ligand I highlighted Lysine (K) residue as yellow. What I want to do is to highlight and draw ...
0 votes
1 answer
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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. ...
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1 answer
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How can I calculate the distance w.r.t. a beta sheet?

Suppose, I have a protein (say, 16PK). and, I want to calculate the distance between one of its alpha-carbons and the nearest beta-sheet. the distance between two strands in a beta-sheet (i, j). How ...
0 votes
1 answer
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Different structures of same protein from two softwares

I used AlphaFold and Swiss-Model to get the structure of a protein (KiSS1R) and then compare them. The structures don't match and I was wondering why the softwares produce models that are different ...
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