Questions tagged [proteins]
Questions relating to proteins, the chains of amino acids that form three-dimensional structures carrying important functions of life. Protein sequence, structure, similarity, domains, etc.
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How to find amino acid sequence of a given protein
Is there a way to look up the amino acid sequence of a given protein? For example, what amino acids are used to produce Amylase? I spent hours googling but to no avail. If that's impossible, how can I ...
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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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2
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missed cleavages combinations generation
I am looking for an R based solution to the following problem:
Trypsin does not cleave perfectly in proteomics experiments. So starting from a protein sequence FASTA I want to generate all possible ...
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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 ...
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2
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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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Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average
I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine... except some of the codon ...
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Good practices for doing sanity checks when parsing multiple PDB files
This is my first time posting to stack exchange, as well as to using data-driven approaches, so please correct me if my questions is not clear enough.
I am trying to parse 200+ .pdb files to extract ...
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KeyError '/n' in Bio SeqUtils Package ProtParam Script
I am trying to run a function from the ProtParam script in the Bio.SeqUtils package. The function is for calculating the instability index of a protein. The code I am using in my script with the pre-...
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How many protein sequences do we usually have for each species?
My question is exactly the one in the title. I add a particular example for more clarity. If I want to study the sequence of protein IkBα, do I find only one sequence or is there a database that ...
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95
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Creating a scatterplot by a json data in js
I have a json file of protein data of mouse and human like
...
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63
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How to get the nucleotide sequence for protein NCBI accession code, programatically?
It is a lot easier in my work to do blast searches against protein databases when I can, since I work with distantly related organisms. But sometimes, I need to work with the actual nucleotide ...
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Histogram plot using R/python with two variables[BC and Control] and their corresponding gene names
How do we plot histogram in R\Python with two variables[BC and Control] and their corresponding gene names examples is below:
Thank you,
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Molecular dynamic simulation, reconstuction of protonation pattern of a protein from PDB file without resolvent hydrogen
I'm trying to build a topology of a protein using GROMACS. The pdb file do not include coordinates of hydrogen atoms. So I was wondering how to assign appropriate protonation states for each residue. ...
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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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To find amino acid substitution from fasta alignment
I have fasta multiple sequence alignment file of protein sequence. I want to look for mutation/substitution in amino acid between query with reference to one query. Is there any R package or any ...
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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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expansions and contractions from OrthoFinder
The input file looks like this, and the complete file can be found here:
...
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What is changed in this PDB file?
I used a tool called reduce to add Hydrogen bonds information to the PDB file.
I used the command:
$ ./reduce -NOFLIP 2GB1.pdb > 2GB1_with_H.pdb
The output file ...
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Searching motifs in sequence and their frequencies
This is a two part question.
I am searching for a motif, and in that search I wanted to also find the total number of sequences in my FASTA file, but the code I wrote is not yielding that please see ...
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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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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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Can the information regarding atomic bonds be interpreted only from atom lines in a PDB file?
The following are the first 14 atoms from the protein 1CRN:
...
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How can I extract the Protein distance map data in Julia?
I calculated the distance between C-alphas using Julia,
but there is no way to extract distance map data from Julia.
I don't even know the data file form, png or csv or etc.
I don't want to extract it ...
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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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finding the frequency of a motif-matching peptide
This question has also been asked on Biostars
I want to find the frequency of each motif-matching peptide.
The sequences are:
...
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finding overlapping motifs to increase length of motif
I am able to find matching motif in my sequence, and I would like to now find overlapping motifs. Basically, after matching my motif, I want to find the 6 amino acids after it. This is the code below ...
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motif searching in a multi-fasta file
I am having trouble trying to search for motifs in a multi fasta file. I have used two techniques one gives me the name of the sequence where the motif is found but doesn't give me the the motif and ...
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138
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finding motifs in fasta file with multiple sequences
I am able to find matching motifs on a single sequence, as well as their position as shown below :
...
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Non-parametric, background-based tests on proteomics data from Proteome Discoverer v2.5?
I am new to proteomics analysis, so apologies if my question is silly! For context, I am working with proteome samples from the postmortem human brain for a case-control study.
Our lab generally ...
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What is the difference between profile and pattern in Prosite?
I found a definition:
"A pattern is thus a qualitative description of a motif in terms of amino acid sequence. The concept of a profile extends this concept, allowing a quantitative description ...
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Retrieval protein definition from accession ID
I have a list of protein accessions:
XP_025107904.1
PVD22034.1
AJA37836.1
How can I obtain the definition of the protein, and the related organism?
Output:
...
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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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How to calculate average BLOSUM62 scores?
I can understand the motive behind the BLOSUM62 matrix, this being a pairwise mutation matrix describing aggregate mutations between the 20 amino acids.
However how would you calculate the average ...
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Select representetive sequence within MSA (protein)
I am trying to pick the best representative sequence from an amino acid MSA. I do not want to use the consensus, as it generates an artificial one. Here is my approach:
I calculate a Percentage ...
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468
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PyMol alignment script
Is there a way write a script in python to use "super" to align proteins from a 2D array? Each row of the array has 2 columns, and for each row, I want to "super" the two proteins (...
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How do I read mmCIF files from Alphafold DB as coordinates to use in replicating their visualization for Unity VR?
https://alphafold.com/entry/Q9Y499
Starting at line 918 of the downloadable mmCIF file, it looks like there might be coordinates in x, y,z:
...
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mass spectrum matching with cyclic peptide and linear peptide
I was doing a simple quiz which I encountered the following two questions related to mass spectrum matching with cyclic peptide and linear peptide.
I have done some preliminary google search, but I am ...
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Multifasta protein alignment
I have around 4000 orthologous proteins for each of 5 species, I'd like to align them and to concatenate alignments. Which tools can I use? And how?
Marco
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How can I remove FASTA sequences with an asterisk inside the sequence?
I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences.
In the example below, I have three sequences:
From this example, I would like ...
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Problem with sequence alignment
I'm trying to find if the peptides in column A are present within the longer peptides of column B.
Pairwise alignment tools take the data from both columns as one string (i.e., TIIDYTNNHYTNNHLEII... ...
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Program for SOV calculation
Are there any programs (web server or installable) out there to calculate segment overlap score (SOV) for protein secondary structures?
Thanks
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How can I parse alternative atom information?
I am trying to parse PDB files.
Say, a PDB file has the following data:
...
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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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What is the basic difference between a protein and a ligand?
Is ligand a type of protein or vice versa?
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Identification of unique chains in proteins by sequence similarity
I'm trying to find unique chains or proteins within their PDB files. Many proteins have multiple chains, but very often they are identical (say, the PDB file consists of 4 homodimers, for example, so ...
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Generate consensus protein sequence from relatively gappy alignment?
I would like to know what would be the best way to generate a full-length consensus sequence?
I want to obtain a single representative sequence from a relatively gappy multiple sequence alignment of ...
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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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What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
N.B. I am not talking about DNA/RNA/genomics. I am talking about protein folding, as it relates ...
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Cytoscape for coloring the nodes in the network
I need to color different categories of the proteins in the interaction network automatically. Is there any way to color each category with a different color in cytoscape? or R?
My input is 2 column ...
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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 ...