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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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 ...
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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. ...
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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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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 ...
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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? ...
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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 ...
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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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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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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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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 ...
CommunityBot
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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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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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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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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 ...
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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 ...
CommunityBot
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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 ...
CommunityBot
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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 ...
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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 ...
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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, ...
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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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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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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 ...
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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 ...
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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(...
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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 ...
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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 ...
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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?
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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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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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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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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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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 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 ...
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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 ?
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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 ...
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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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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:
...
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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.
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Protein ligand docking: how to convert <protein>.pdb to <protein>.maps.fld?
Hello I'm helping to develop a cloud docking tool for screening compounds, similar to Swissdock but with mass throughput and GPU optimizations.
Specifically helping screen existing drugs against ...
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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 ...
M__♦
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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 ...
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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 ...
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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 ...
CommunityBot
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Generate ligands candidates based on protein shape
Recent approaches to novel drug design using machine learning (ML) and deep learning, often involve generating hundreds of potential ligands which are later tested by docking with a target protein and ...
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Python script to calculate properties of amino acids and storing them in matrix
I want to make a python script that can get as input sequence of N amino acids, and the output is a matrix of Nx6 containing 6 features.
The features are:
Computed volume
Hydrophobicity
Surface ...
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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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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 ...
