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.

22 questions with no upvoted or accepted answers
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4
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1answer
64 views

Is there a modern alignment tool tailored for transmembrane regions?

I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information ...
4
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0answers
210 views

Map domain names from UniProt bed files to domain accessions

I want to get a bed file mapping human protein domains to the human genome. UniProt actually offers such a thing here. The problem, however, is that the file doesn't include any kind of domain ...
2
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0answers
125 views

What exactly does each of InterPro, PANTHER, Pfam bring to the table individually in classifying a protein?

I would be very grateful if somebody could sketch out the methods Pfam and PANTHER use to assign a family to a given protein and how they are different. My (cursory) understanding is that InterpProp ...
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0answers
107 views

How to get the GO information for all the human genes?

I would like to retrieve a list of all the human genes and their proteins’ functional classification. The Gene type attribute on ensembl.org is not specific ...
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0answers
12 views

How to find disease association of disgenet with string db in homo sapiens

I want to work string-db to read the protein-protein interaction from it and I look up disease association from disgenet but the Ids do not seem to match-up and I do not know what to do. for example ...
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0answers
19 views

Why ace2 is not included in SARS-COV-2 PPIN map?

I'm doing my master's thesis on drug repositioning for sars-cov-2 using AI more specificaly network medicine, I found only one PPIN map from Gordon et al. but it doesn't include the ace2 protein which ...
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0answers
26 views

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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0answers
36 views

Error while splitting PDBQT file

I am trying to split to a pdbqt file containing 178 compounds into individual pdbqt files. I have been using the Autodock Vina_split.exe file to split the multiple entry file however I keep running ...
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0answers
17 views

Residue coevoution from position wise residue preferences rather than multiple sequence alignments

Hello experts in residue coevolution analysis of proteins, I am looking for a way to calculate residue coevolution (coupling scores) between all pairs of residues of a protein. The issue is that ...
1
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0answers
40 views

Is there a software that can predict protein-DNA binding?

Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
1
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0answers
33 views

Available Protein sequence alignment dataset and HMM model

It may better to move the question here. I am new to biology and I find my algorithm may be used in the Protein sequence alignment, since it is a henced HMM model. I find that people use HMM to ...
1
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0answers
83 views

How can I interpret multiple alignment results?

I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE. I would like to ask if consistency score plays any role in the interpretation? I ...
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0answers
25 views

What are the meanings of these transcript ids?

I have three types of transcripts for Rosa chinensis "Old Blush" homozygous genome v2.0 from GDR genome browser. ...
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0answers
14 views

Finding the conserved region of protein in a given set of Kingdom

We have to find the conserved region of proteins in a given set of kingdom and we have to give more weightage to distantly related organism. What approach I should take to solve this problem?
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0answers
12 views

"No records to view" error in the "Drug and Drug Target Mapping" PDB's search engine

I'm using the "Drug and Drug Target Mapping" search engine (http://www.rcsb.org/pdb/ligand/drugMapping.do). I've noticed that there are some drugs (generic names) that if they appear in the query, the ...
0
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0answers
76 views

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 Polarity ...
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0answers
17 views

phosphosite nomenclature and conversion (phosphoproteomics)

I have a dataset containing the following kind of phosphorylation sites nomenclature: ...
0
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0answers
35 views

How can I get properties from each one letter amino acid?

Im using python and wish to get properties from each one letter amino acid? I mean M(Met) => Density:1.340, MW:149.21... The RDkit methods atom.GetSymbol(), atom.GetDegree() permit this and I am ...
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0answers
6 views

Mutated residue number shown wrong in foldX yasara

I am trying to mutate phenylalanine 274 position in Uracil DNA glycosylase with alanine. The pDB file has the protein starting from 82nd residue. After the repair the console shows FA161A. The residue ...
0
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0answers
46 views

Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions

I'm trying to programmatically replace a set of amino acid residues on an MSA with a "Z" from a list of unaligned positions. Any ideas on how I could do this? Input: a list of unaligned ...
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0answers
37 views

Please help me with my command!

I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
0
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1answer
46 views

Automating download of results of Drug and Drug Target Mapping

The drug and drug target mapping tool shows the top 3 PDB IDs for each drug based on the drug target sequence similarity search and ligand id search. Is there a way to get all the PDB ids of the drug-...