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 do we simulate with molecular simulation of proteins? [closed]

I know some: Secondary structure prediction Tertiary structure prediction protein-surface interaction test protein-protein interaction test protein-ligand binding test What else do we simulate? ...
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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 ...
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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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Heat map of protein expression from normalized abundance

This is a follow up to my question posted here Processing proteomics data In relevance to my research, I've been looking for proteomics data (control vs. diabetic) and I found a dataset in the article ...
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Running into an error when loading Flexaid on PyMol 3.7

I have attached a screenshot from terminal, which is the result of me attempting to run Flexaid on my Mac. I was wondering if anyone knows why this isn't running? Thanks
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3 answers
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How to identify [hyper]thermophilic proteins by BLAST search?

I need to find homologs of certain proteins by BLAST search or similar. But I want filter (select) homologs from organisms that are classified as thermophilic or hyperthermophilic. I am wondering if ...
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Unable to install OpenBabel

I am working on building a script that tests the binding affinity of protein-ligand pairs generated by our ML model as positive/negative binding annotations. One of the steps in doing so requires the ...
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Processing proteomics data

[this question was also asked on BioStars] 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 marked ...
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  • 125
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2 answers
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Help using BioPython's IC_Chain functionality for getting protein 3D coordinates from torsion angles

I have been successfully using BioPython's functionality for extracting protein torsion angles using the IC_Chain module. However, I am currently looking to use the ...
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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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Is it possible to reconstruct an MSA with PSSM?

I am thinking of reconstructing an multiple sequence alignment (MSA) of protein sequences from a position-Specific Scoring Matrices (PSSM). Is it possible? I suppose co-evolution information is lost ...
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On the same strand, for the same gene, can exons be overlapping?

I want to get a set of exon regions for each protein coding gene. I extracted a set of relevant information (chromosome, start, end, gene ID, gene name, gene type, exon number and exon ID) from a GTF ...
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BioPython internal_coords module returns different dihedral angles for the (seemingly) same protein structure

I am using the internal_coords module from BioPython in order to compare dihedral angles of two different conformations of the same protein. The conformations are ...
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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 ...
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Why does this modification site file contain duplicate sites and multiple related proteins?

The data below is coming from a MaxQuant post-translational protein modification (PTM) site file. Why does it contain duplicate sites (yellow) and proteins (cyan)? Source data http://ftp.ebi.ac.uk/...
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Identify side chain atoms in BioPandas dataframe

I am currently implementing some metrics I could use for comparing two conformations of the same protein in Python. For example, I know I could use the RMSD of all protein ATOMS in BioPandas using ...
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Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python

I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command ...
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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
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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 ...
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3 votes
1 answer
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Relationship between entries for same UniProt Id

I was playing around, looking at some AlphaFold predictions for certain proteins and I realized that sometimes the sequences of aminoacid look very different for the same UniProt id. For example, 15C8 ...
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Protein-coding gene evolution age and species divergence time: are they correlated?

Is it possible to infer protein-coding gene evolution age by species divergence time? For example, species A diverged 300 million years (MYA) ago from its common ancestor with species C, whilst ...
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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 ...
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2 votes
2 answers
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Is there a publication database or search engine offering geneID or UniProtID correlation?

Do we have a publication database or search engine that offers geneID or UniProtID correlation? For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
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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-...
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What is the cutoff distance in this algorithm?

In the following article: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements What are the minimum and maximum cutoff distances in this algorithm? Also,...
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PDBQT file format

I am trying to understand the source code of the AutoDock Vina, but as I am new to the field of Bioinformatics it is a little hard to understand. It seems like they are using a tree data structure to ...
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Where can I get info about A. thaliana proteins' locations?

I have a list of A. thaliana proteins and I'd like to know their location in the cell. I've found SUBA but they seem not to share their dataset and only allow queries through their website. It's ...
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Permutation Function of 4 amino acid sequence on Bash shell

How can I write a Programming Language to construct about 160000 tetrapeptide from the 20Amino acids using permutation on Bash Shell.
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CITEseq different sequencing depth normalization -- Seurat

New technician ruined his first 10X CITEseq experiment on cells counting level and the ratio between replicates is 14k:2.2k:0.8k ncells. How should I now normalize protein data (ADT) from experiment ...
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How can I identify acceptor and donor atoms using BioPython?

I know how to traverse through structures, models, residues, and atoms in a protein chain using BioPython (which is very easy). How can I identify donor and acceptor atoms in a chain?
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How can I programmatically add Hydrogen to a PDB structure using BioPython?

I need to programmatically add Hydrogen atoms to a PDB file (say, 16PK.pdb) using BioPython. What algorithm should I use for this?
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1 answer
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Organelle genome genes

How can I get all proteins coded by mitochondrial genome or plastid genome from UniProt. I see UniProt has multiple filtering and search parameters but I could not distinguish between proteins/genes ...
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How can I calculate the distance w.r.t. a beta sheet?

Suppose, I have a protein (say, 16PK). and, I want to calculate the distance between one of its alpha-carbons and the nearest beta-sheet. the distance between two strands in a beta-sheet (i, j). How ...
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1 answer
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Different structures of same protein from two softwares

I used AlphaFold and Swiss-Model to get the structure of a protein (KiSS1R) and then compare them. The structures don't match and I was wondering why the softwares produce models that are different ...
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Why is there a drop in the publication's rate of protein-sequences in UniProtKB/SwissProt

UniProt provides two databases 1: UniProtKB/TrEMBL (TE) with entries for which the annotations are derived from the European Nucleotide Archive. UniProtKB/SwissProt (SP) with entries for which the ...
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2 votes
1 answer
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Is there any database about the abundance of proteins in urine of healthy patients?

I have a dataset about adundance of urine proteins from cancer patients. I would like to compare these abundance levels to healthy patients' urine proteins. However I don't have any data with healthy ...
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Is "Assignment" a part of the "Prediction" process? [duplicate]

I am talking about secondary structure assignment and secondary structure prediction of proteins. Is "Assignment" a part of the "Prediction" process?
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1 answer
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Translate all reads in a .fastq into protein sequence from deep mutational scanning experiment

I'm working with paired-end NGS reads from an Illumina platform. The sequences I have are all of the same gene, but have one or more substitution mutations each. Here is a rough workflow for ...
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1 answer
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How can I calculate the distances between two specific residues of a protein from a PDB file?

Suppose, we have a protein (16PK). We are considering a 5-residue segment/window. If we assume ASN10 to be the ...
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1 vote
1 answer
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What does the following diagram represent?

Suppose, the following is a diagram of a protein's polypeptide chain: What does this diagram represent? What are the letters A, E, M, W, L, N, S, etc. represent? (I suppose these are amino acid ...
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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 Polarity ...
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2 votes
2 answers
154 views

What is the difference between Assignment and Prediction?

I am absolutely new to Structural Bioinformatics (I only started last week). I am working on the secondary structure assignment/prediction (actually I am not sure) of proteins using ML. When it comes ...
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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 ...
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4 votes
1 answer
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How do I get GO annotations for a list of UniProt IDs?

I have a list of UniProt ids that I want to get Gene Ontology annotations for. I need this information because I want this high-level information as an input to a neural network. The model I wish to ...
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1 vote
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How to calculate RMSD and binding energy from the already docked ligand-receptor

I have the following PDB file that looks like this. It is downloadable here. This PDB already contains ligand and receptor together. The red molecule is the ligand and the yellow is the receptor. They'...
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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 ...
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3 votes
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Convert .smp from CDD into HMM file [closed]

Is there a method or tool to convert a .smp file from CDD (Protein Domain File) into a HMM file? I downloaded the CDD files from the FTP site and am more familiar with domain searching with the HMMer ...
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1 answer
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Holistic enzyme activity determination with computation [closed]

I'm currently working on a program which will determine the activity difference between an original enzyme and a variant with just 1 or 2 variants. Of course, I'm not talking about the "kinetic ...
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1 vote
1 answer
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How to get 2d/3d structural coordinates from a PDB file?

Is there a way we can get 2d/3d structural coordinates like in (x/y/z) manner from a pdb file. I have looked a believe that the coordinates are in below line: ...
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