Questions tagged [interactions]
The interactions tag has no usage guidance.
18 questions
3
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0
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LigPlot (LigPlus) Giving Different Interactions on Command Line and GUI
I am trying to determine the interaction of the targeted amino acid with other amino acids, but I am having trouble. When I pass a PDB file of a protein that has ligands, I can see the interactions. ...
- 31
2
votes
0
answers
62
views
2D diagram of intermolecular interactions in R
I've docked a large inorganic compound (receptor) with an organic molecule that isn't a protein (ligand). I wanted to see the interaction between them in a 2D diagram, but BIOVIA Discovery Studio (DS) ...
- 31
2
votes
0
answers
13
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Find Lipidic Mediator receptors
I want to study the ligand-receptor interaction and I am searching for lipidic ligands( mediators), I have found 16 so far. Does anyone know any database where I could find more lipidic ligands. I was ...
0
votes
0
answers
12
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Plant signaling pathway interconnections
I'm sorry for having such a juvenile question, but I'm still new in bioinformatics, and I was wondering whether there is any tool able to perform the task I'm dealing with now.
Here is a short ...
- 1
0
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1
answer
196
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Running GSEA or comparable analysis with multiple variable interaction?
I am working with an RNA-seq dataset generated from a complex experimental design. Our main question is focused on the interaction between two variables, one (INJ) with two conditions (L,S) and the ...
- 45
0
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1
answer
55
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Is it possible to predict protein-ligand binding kinetics using machine learning? [closed]
I would like to work on a project that involves the prediction of protein-ligand binding kinetics. What might be the feature that is relevant for the prediction?
3
votes
1
answer
67
views
Why is there a chloride ion in this 3D model?
Here we have a 3D model of a sequence that match with this sequence
VVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK
in Blast
the 3D structure is here
Why is there a chloride ion in this 3D model?
1
vote
1
answer
569
views
Looking for a way to download all pdb files that detail a protein-drug complex
I am looking for a way to download all pdb files that detail a protein-drug complex.
While I could download the entirety of the pdb and search manually (or maybe write a script to discard all ...
- 121
0
votes
1
answer
81
views
How to predict protein binding to ligands?
I want to predict from protein sequence if the protein binds to metal, nuclear or small ligand. How can I do this ? Which features are relevant if I want to use them in a machine learning algorithm ?
- 1
1
vote
1
answer
126
views
ipfam or pfam domain-domain interactions
I'd like to download domain-domain interactions that were in ipfam (which doesn't seem to be up-and-running anymore).
for an example of what I would like to be able to download via ftp or another ...
- 113
2
votes
1
answer
56
views
How to get all chemical compounds that interact with a given protein target?
I want to get all Pubchem Chemical compounds (CID) that interact with a given UniProt target. I have a list of UniProt targets and I need to study the relationship between these targets and chemical ...
- 35
3
votes
1
answer
138
views
finding RNA-protein physical interaction
We all know that for physical protein-protein interaction, we need to find the distance between residues from PDB file of that interaction (finding distance between carbon alpha, carbon beta or ...
- 777
1
vote
1
answer
40
views
Finding new drug-protein targets/interactions using a known one as base
Given a known interaction of a molecule with some proteases (having X-rays images too) is it possible to predict interactions with other proteins either using their 3D structure or not?
If anyone ...
- 575
0
votes
1
answer
48
views
Where did the BIND website go?
I was trying to reach the BIND (Biomolecular Interaction Network Database) but the website is down.
Where can I find something similar? Has this platform moved somewhere or what?
4
votes
1
answer
72
views
Using signal peptide and the expression levels of signal recognition particle in secretome analysis
I have not found any work which investigates assessment of differences in levels of secreted proteins by taking advantage of differential expression of the genes which mediate the secretory pathway.
...
- 524
3
votes
1
answer
125
views
Building network for biomarker interaction analysis
I am looking for advice on how to best approach a problem I am faced with.
I have a dataset of numerous degradative biomarkers, clinical information and various other measures (from clinical trials)....
- 131
5
votes
2
answers
264
views
Tool for predicting interactions in the cell
What tools are available to predict, based on the structure of a certain protein, its interactions within a cell?
For example, I am considering the split GFP protein and I am trying to predict if ...
- 524
4
votes
4
answers
162
views
What are the standard ways to visualize protein-protein or gene-gene interactions?
I would like to visualize this interaction list. Is there an online/web based way to do it? Is there a way to analyze the data?
Assuming I have exported the list into lines such as:
...
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