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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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5 votes
1 answer
53 views

How can I compute distance matrices from a PDB file?

I want to compute the distance matrix from PDB files. So, I wrote the following Python code using BioPython. ...
user366312's user avatar
2 votes
1 answer
19 views

How can I search globular proteins by residue count in the RCSB databse?

I want to find some globular proteins with some of the longest individual chains that have all three types of secondary structures,, namely helix, sheet, and loop. So, I tried the following search: ...
user366312's user avatar
4 votes
1 answer
30 views

Protein atlas rna-seq vs protein expression region missmatch

I am finding a levels of gene expression in protein vs rna seq not correlating in protein atlas for a gene of interest. In rna-sequencing there is a high level of expression mainly in the brain, in ...
Professional Pigeon's user avatar
1 vote
1 answer
41 views

Is there any standardized and ready-to-use dataset available online for download regarding protein geometry? [closed]

I want to do ML model training and data analysis for secondary structure prediction. Is there any standardized and ready-to-use dataset available online regarding protein geometry? For example, the ...
user366312's user avatar
2 votes
1 answer
88 views

Why do we need seondary structure detection algorithms?

There are many secondary structure prediction and assignment algorithms (e.g., DSSP, STRIDE, etc.) available. On the other hand, I see that PDB files have secondary structure information available in ...
user366312's user avatar
4 votes
0 answers
88 views

Why are DSSP and STRIDE considered reference algorithms, and why do people continue to use them?

I am working on globular protein secondary structure assignments. The purpose of my project is to design an improved algorithm for secondary structure assignment. I know two tools: ...
user366312's user avatar
3 votes
1 answer
42 views

How can I detect secondary structures in a protein using a hydrogen bond detection algorithm?

Suppose I have a protein chain. And I have a hydrogen bond detection algorithm that can detect hydrogen bonds in a protein chain. Say, the name of the algorithm is HBDA algorithm. How can I detect ...
user366312's user avatar
2 votes
0 answers
12 views

Accuracy of large peptide fragment in LC-MS/MS

Peptide digestion leads to generation of small peptides (ideal) as well as some large peptides (3-4kDa). The large peptides often don't fly well and therefore do not detect well. Does it affect the ...
Science123's user avatar
1 vote
1 answer
34 views

Fragment mass tolerance in proteomics analysis

Proteomics newbie here. I am using proteome discoverer software to analyze the fragmentation of a chemically modified single protein. In my understanding, when we set the Fragment mass tolerance to ...
Science123's user avatar
1 vote
0 answers
43 views

how to annotate the effect of a genomic variant to predict what the resulting protein is?

Spoiler: This is probably a theoretical question. But, of course, if you have any tool that does this I will be extremely happy. So, I have WGS data for an organism O, both wild type (WT-O) and ...
gabt's user avatar
  • 348
2 votes
0 answers
40 views

How to create a dataset of contact maps of homologous proteins?

Disclaimer: I am a machine learning researcher working on network science and want to use proteins to test an algorithm of mine using real-world data. My bioinformatics knowledge is minimal. I need to ...
Tendero's user avatar
  • 121
2 votes
0 answers
38 views

Method for reproducing minimal, cartoon-style protein structure visualisation

I recently came across a preprint ( DOI, PDF link ) that has some figures of protein structures in a style that I have not seen before. To me it appears easier on the eyes and less noisy than the ...
asimov's user avatar
  • 21
0 votes
0 answers
21 views

Does the value of RMSD have any impact on my vina results? Are results with RMSD greater than 2 unreliable?

This is part of my result.I saw someone saying that Vina docking results with rmsd greater than 2 are unreliable, but I don’t know how to judge.Help,plz!
Ni Wu's user avatar
  • 1
1 vote
0 answers
10 views

How to find a database for proteins that bind to different molecules and have different binding sites?

I'm doing a study in which I'm trying to analyze the effect of molecules (ligands) on binding sites of proteins. Therefore, I'm trying to find a database in which the proteins bind to multiple ...
FakeNTAccount's user avatar
1 vote
0 answers
22 views

How do I do "protein culling"?

I am working on a novel protein secondary structure detection algorithm using machine learning. As far as I understand, online protein databanks (e.g., RCSB, etc.) have a huge collection of proteins (...
user366312's user avatar
2 votes
0 answers
43 views

Protein conservation analysis with trident scores in R script

I am currently working on analyzing protein conservation across amino acid positions using Trident scores as output from the MstatX tool. I have 40,000 Trident score files, each containing amino acid ...
C. Valera's user avatar
1 vote
0 answers
15 views

Exploring Amino Acid Patterns in Proteins Through N-gram Analysis [closed]

In our recent research, we delved into the amino acid composition of protein sequences by applying n-gram analysis techniques. By examining the distribution of n-grams ranging from 1-gram to 11-gram, ...
anatol's user avatar
  • 111
3 votes
0 answers
22 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
2 answers
82 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
4 votes
2 answers
82 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
28 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
39 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
47 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
59 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
79 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
2 votes
1 answer
80 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
148 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
128 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
1 vote
1 answer
134 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
  • 121
0 votes
0 answers
79 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
128 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
87 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
53 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
59 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
55 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
89 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
111 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
238 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
  • 2,232
2 votes
2 answers
133 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
  • 1,007
-1 votes
1 answer
123 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
4 votes
3 answers
328 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
62 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
379 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
73 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
43 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
220 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
  • 163
1 vote
2 answers
71 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
51 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

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