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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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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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 ...
terdon's user avatar
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Setting up MaxQuant parameters for processing proteomics data

This is a follow up to my previous question here. In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article "Diabetes causes ...
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PSSM Matrix in PSI-BLAST

After running PSI-BLAST one obtains a profile matrix with this header: A R N D C Q E G H I L K M F P S T W Y V How does PSI-...
Caterina's user avatar
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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 : ...
thole's user avatar
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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 ...
MrMorgotheron's user avatar
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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 ...
dallas_engineer's user avatar
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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
Balint Biro's user avatar
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What is coarse-grained modeling of proteins?

I need beginner-level study materials for coarse-grained modeling of proteins. Can anyone supply me with entry level resources besides the Wikipedia article? Background Coarse grain protein modelling ...
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Why isn’t ace2 included in SARS‑CoV‑2 PPI map?

I'm doing my master's thesis on drug repositioning for SARS‑CoV‑2 using AI more specifically network medicine, I found only one human protein-protein interactions (PPIs) map from Gordon et al. The ...
hpPh's user avatar
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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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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
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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
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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
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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
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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 ...
Aureo André Karolczak's user avatar
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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 ...
Nithya Chandramohan's user avatar
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How to identify different protein domains using HHpred

I am new to HHpred/ analyzing proteins so bare with me. I have been given an uncharacterized protein, whose FASTA sequence I have obtained from Uniprot. I am looking to do the following by using ...
microbeprincess's user avatar
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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 ...
Anas Jamshed's user avatar
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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 ...
nima moradi's user avatar
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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 ...
user10169's user avatar
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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 ...
ibio_rep1's user avatar
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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 ...
user345394's user avatar
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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 ...
Anthony Guterres's user avatar
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100 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 ...
Qinsheng Zhang's user avatar
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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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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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16 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?
Mritunjay's user avatar
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"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 ...
Adrian Smith's user avatar
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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
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2 answers
39 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
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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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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
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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. ...
user17203's user avatar
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How can I convert protein distance maps and sequences to a pdb files?

How can I convert protein distance maps and sequences to pdb files? For the same problem, in the case of a model predicting the structure of a protein, such as AlphaFold, how do we convert the ...
이명훈's user avatar
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1 answer
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plot the relation between RMSD and free energy

how can i plot the relation between rmsd and free energy like the image i attached as i need to find the most stable conformation structure for my cycle peptide after finishing REMD simulation
sam's user avatar
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Chimera- How to go about changing the threshold of the EM map?

It is my first time using Chimera. I have uploaded a PDB file on to Chimera and opened it up on the software. I need to change the threshold of the EM map so that I can analyze what the EM map would ...
microbeprincess's user avatar
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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 ...
MH Lee's user avatar
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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 ...
AlphaQueUp's user avatar
0 votes
1 answer
63 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-...
Adrian Smith's user avatar