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 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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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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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 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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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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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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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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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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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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Programmatically adding hydrogen and remove water to multiple PDB files
I'm trying to dock a ligand to several hundred PDB files (receptors).
I thus need to prepare the those PDB files like removing water and adding hydrogen.
I can do that manually using Autodock or Pymol....
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How to tell if our ligand-protein docking is good from AutoDock Vina's result
I have perform a ligand-protein docking using Autodock Vina.
The result of the docking looks like this:
...
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How to extract subset of protein structure (PDB format) file based on a subsequence of that protein
I looking at a particular protein structure called 2LY4 accessible from RSCB PDB website.
The corresponding fasta sequence for that structure is this:
...
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How to index residues by icode in biopython?
I am indexing a structure by the code below:
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How to introduce point mutations in a protein structure?
I want to introduce point mutations to a protein PDB file and automatically predict the 3D coordinates of a new amino acid residue in the mutated protein.
I used interactive Schrodinger's Maestro tool ...
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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 ...
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Holistic enzyme activity determination with computation [closed]
I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
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How to get 2d/3d structural coordinates from a PDB file?
Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file.
I have looked a believe that the coordinates are in below line:
...
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PDB: Download all biological assemblies
I was wondering if it is possible to download all biological assemblies from the PDB at once (so not the standard asymmetrical files). For example, I want a file containing the coordinates of all ...
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Java Protein Comparison Visualisation
I have project where I am required to build a visual analytics tool into an existing Java project to visually compare and analyse protein sequences from SwissProt, GenBank, EMBL etc. (downloaded from ...
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How to choose docking score cutoff?
I made a virtual screening of a large database (~5M) and want to filter ligand structures for further more accurate screening (from Schrodinger HTVS to SP resolution). My next step is to define a ...
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How do you calculate the top L/5 score?
I am currently investigating how to predict protein structure and contact map predictions. There, I see things like top L/5 and top L/2 scores as a way to evaluate the contact map. What formulas do ...
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How can atomic RMS differences / atomic RMS distributions help us understand the structure of a protein?
For example, I have a paper that says: "the atomic RMS distribution about the mean coordinate positions is 0.41 +/- 0.04 A for the backbone atoms and 0.82 +/- 0.04 A for all atoms"
And I ...
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Get protein names corresponding to PDB ID
I have a list of about 4000 PDB IDs and would like to get the actual names of the proteins (e.g. lactate dehydrogenase, cytochrome c). I tried the batch header section at the Protein Databank Download ...
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How to see if a gene is the product of copy number variation?
Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals.Copy number variation is a type of ...
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How many entries in PDB have SS bonds?
Is there a way to figure out what percentage of entries in PDB have SS bonds?
In addition, what other types of bonds in PDB may be worth looking into (not H bonds)?
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How does sequence alignment help with protein folding prediction? [closed]
I've been seeing using sequence alignment to help with prediction of protein folding, but am unable to understand why. Google returns other research papers for these search terms, hence I'm hoping the ...
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What programs account for structural alignment of different parts of distant homologs which have significant structural differences?
If there is a need to perform structural alignment of different parts of distant homologs, which program one should use?
Since distant homologs often have significant structural changes, meaning the ...
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How are different forcefields developed/evaluated?
The Rosetta software can use a variety of different energy functions:
Ref2015
GenPot
Beta-Nov16
How are these energy functions developed and validated? Is it common to do a single protein design ...
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B-factor analysis in nanobodies
I am doing my research on nanobodies. Currently, I am trying to do a comparison study of the flexibility of CDR loops using B-factor values. I would like to know if there is any statistical analysis ...
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Delete chains from a protein
We have a docking target protein with multiple chains (A,B and C). However, I just need chain A. How can I delete the 2 other chains from the docking target protein.
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Issues with AutoDock Vina
I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
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How to implement SEG (Wootton and Federhen ,1993) algorithm?
I want to implement SEG in my MATLAB environment and I'm relying on Wootton and Federhen (1993)
Reading the article I cannot succeed to understand what kind of process I have to implement in order to ...
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Extract only the amino acid residues on the surface of protein structure data
I'd like to use protein structure data from PDBs visualized by Chimera to do two things.
I'd be happy to learn the appropriate tools and methods.
・Mapping information about amino acids present on ...
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Do I need to fill in missing side chains and loops before protein-ligand docking for VLS?
I am going to screen a set of small molecules against a CYP450 2C9 protein target. The structure I am using exactly is 5A5I. Do I need to fill in missing side chains and loops before performing VLS? I ...