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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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 ...
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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?
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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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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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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 ...
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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 ...
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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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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 ...
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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, ...
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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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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 ...
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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 ...
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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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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 ...
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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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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 ...
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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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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 ...
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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 ...
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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 ...
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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
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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 ...
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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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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 ...
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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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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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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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Permutation Function of 4 amino acid sequence on Bash shell

How can I write a Programming Language to construct about 160000 tetrapeptide from the 20Amino acids using permutation on Bash Shell.
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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: ...
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1 answer
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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 ...
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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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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 ...
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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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Site Mutations in a 3D protein structure to locate the core of mutations

I have a pdb file for a protein (3D structure predicted by a tool) and around hundreds of known point mutations in the protein. I want to visualize the protein with all the mutations to see the hub of ...
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Does the Protein Data Bank contain the estimated distances obtained using NMR spectroscopy?

From the Wikipedia entry on the Protein Data Bank (PDB) (emphasis mine): Most structures are determined by X-ray diffraction, but about 10% of structures are determined by protein NMR. When using X-...
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GROMACS RMSF Result Analysis Problem

This is RMSF for protein from GROMACS after 100ns simulation- I have few questions- Residue numbers are starting from 1650 to 1850, has it ignore LIG and HOH as residues? There are three lines, so ...
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What does the following diagram represent?

Suppose, the following is a diagram of a protein's polypeptide chain: What does this diagram represent? What are the letters A, E, M, W, L, N, S, etc. represent? (I suppose these are amino acid ...
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PyMol: Output Polar Contacts Between Chains to Text File

I am new to PyMOL but have a very specific task that I need to do. I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A and all ...
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FoldX PositionScan functions only works for certain position inputs

I'm using the PositionScan function in FoldX 5.0 to calculate delta delta G for some mutants. I'm working with the command prompt in Windows 10. For some reason, this function will only return output ...
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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 ...
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programmatically select and label peptides within pdb file

I have a pdb file of a protein structure, and I would like to programmatically select certain peptides and label them in an annotated pdb file output, so that when the output pdb file is opened again ...
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How are tertiary protein structures represented in computers?

What data structure is used in representing protein structures in computers so that we can apply algorithms? Matrix or Graph or tree? P.S. I am absolutely new to Bioinformatics.
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How to show that one docking is better than another with Pymol visually

I have the following docking results: Dock_1 has better energy score than Dock_2. What I want to do is to show with Pymol that <...
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2 votes
2 answers
160 views

What is the difference between Assignment and Prediction?

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 ...
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1 vote
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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'...
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