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.

Filter by
Sorted by
Tagged with
3 votes
0 answers
21 views

Q8 Accuracy Evaluation metric mathematical expression used in Protein Secondary Structure Prediction

I am working on Protein Secondary Structure Prediction using Recurrent Neural Network (GRU) model. I came across few open source projects which already worked on the similar problem. All of them are ...
Muhammad Usman's user avatar
3 votes
1 answer
66 views

What is the best way to acquire protein isoform sequence alignment?

[Update] Thanks @terdon. To clarify my question: I have a bunch of protein isoforms sequences (produced by the transcripts in the figure) and I want to align protein products (e.g., proteins produced ...
Jen Marylin's user avatar
3 votes
1 answer
53 views

probability of finding a 5 amino acids in a row within a proteome

How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues. The probability of a ...
saplingmagic's user avatar
0 votes
0 answers
18 views

Seeking Advice on Acquiring Clean Experimental data comprises of proteins for FDR Estimation

I am a bioinformatics student doing my research on top-down mass spectrometry-based proteomics and seeking some guidance on acquiring very clean experimental data with known true positives and false ...
Ayesha's user avatar
  • 1
0 votes
0 answers
25 views

Best Library for 3D Protein Structure Visualization and Annotation

I have a background in Computer Science and have recently gotten very interested in the field of Protein Engineering. I am trying to build a web app which displays the 3D structure of a protein when I ...
Katherine's user avatar
0 votes
1 answer
30 views

tBLASTn vs NCBI TSA

Is there a way to blast my proteins against all the TSA (Transcriptome Shotgun Assembly Sequence Database) belonging to a specific taxonomy using command line? Thanks, Marco
Marco's user avatar
  • 161
0 votes
0 answers
29 views

Generating force-fields for ANY residue

Is this possible to generate force fields for any residue in my .pdb file? I am trying to generate conformations for the proteins with arbitrary residues binded to it from .pdb files using OpenMM, but ...
JaktensTid's user avatar
1 vote
0 answers
58 views

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 ...
Omar Shehab's user avatar
0 votes
2 answers
50 views

How long should it take to cluster Uniref?

I have the Uniref90 dataset containing around 76M sequences. I have made modifications to all sequences based on a reduced amino acid alphabet. I am trying to cluster it again at 90% identity. I am ...
GIONII's user avatar
  • 11
1 vote
1 answer
60 views

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? ...
user18494's user avatar
1 vote
0 answers
25 views

What are some good miRNA databases?

I am writing a project proposal for my boss and it is on codon usage bias in the dystrophin protein and the spectrin-like repeats found in a hmmscan file using the longest dystrophin isoform protein ...
Rachel Sweeney's user avatar
1 vote
0 answers
64 views

Renumbering atoms in PDB using OpenBabel

I'm trying to add polar hydrogens to protein (PDB ID 3l3l cleaned from water and ligands) and convert it to PDBQT using OpenBabel by: ...
Evgenii's user avatar
  • 11
1 vote
0 answers
109 views

How can I compute energy from a protein PDB file?

Suppose I have a protein PDB file and want to compute energy using the following formula from the coordinates in the file. How can I do that? Sometimes people suggest using the ...
user366312's user avatar
0 votes
1 answer
60 views

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 ...
Nemo's user avatar
  • 111
0 votes
0 answers
76 views

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: ...
MTG's user avatar
  • 147
3 votes
2 answers
125 views

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 ...
Klemens Fröhlich's user avatar
1 vote
1 answer
64 views

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 ...
Aureo André Karolczak's user avatar
3 votes
2 answers
52 views

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 ...
user366312's user avatar
1 vote
1 answer
54 views

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 ...
Sudoh's user avatar
  • 217
0 votes
0 answers
53 views

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 ...
Priyanshu Gupta's user avatar
3 votes
1 answer
85 views

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-...
Z_Gonzalez's user avatar
1 vote
2 answers
108 views

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 ...
HelpNeederStudent's user avatar
-2 votes
1 answer
178 views

Creating a scatterplot by a json data in js

I have a json file of protein data of mouse and human like ...
Zizogolu's user avatar
  • 2,148
2 votes
2 answers
93 views

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 ...
Laura's user avatar
  • 909
-3 votes
1 answer
116 views

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,
Mahendra Singh's user avatar
0 votes
0 answers
15 views

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. ...
user17203's user avatar
4 votes
3 answers
321 views

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(...
Amal's user avatar
  • 81
-1 votes
2 answers
57 views

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 ...
Shweta Kumari's user avatar
0 votes
2 answers
306 views

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 ...
Amal's user avatar
  • 81
2 votes
2 answers
61 views

expansions and contractions from OrthoFinder

The input file looks like this, and the complete file can be found here: ...
user3523406's user avatar
1 vote
1 answer
40 views

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 ...
user366312's user avatar
4 votes
2 answers
206 views

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 ...
thole's user avatar
  • 143
1 vote
2 answers
69 views

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 ?
arinjoy datta's user avatar
1 vote
1 answer
50 views

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: ...
user366312's user avatar
1 vote
2 answers
32 views

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: ...
user366312's user avatar
0 votes
1 answer
30 views

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 ...
bamblebee's user avatar
4 votes
1 answer
379 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 ...
user366312's user avatar
0 votes
1 answer
98 views

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: ...
thole's user avatar
  • 143
2 votes
2 answers
35 views

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 ...
thole's user avatar
  • 143
2 votes
2 answers
257 views

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 ...
thole's user avatar
  • 143
2 votes
1 answer
198 views

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 : ...
thole's user avatar
  • 143
2 votes
1 answer
180 views

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 ...
Kelly's user avatar
  • 21
2 votes
0 answers
270 views

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 ...
MrMorgotheron's user avatar
2 votes
1 answer
33 views

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: ...
Marco's user avatar
  • 161
2 votes
1 answer
332 views

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 ...
dallas_engineer's user avatar
3 votes
2 answers
181 views

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 ...
Nilay Lale's user avatar
2 votes
1 answer
660 views

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 (...
Jennifer S.'s user avatar
1 vote
1 answer
88 views

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: ...
webNoob13's user avatar
  • 145
1 vote
1 answer
153 views

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 ...
kevin's user avatar
  • 141
1 vote
1 answer
36 views

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
Marco's user avatar
  • 161

1
2 3 4 5