Questions tagged [interactions]

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1answer
59 views

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 ...
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1answer
28 views

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
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1answer
40 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
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1answer
143 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 ...
0
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1answer
57 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
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1answer
67 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 ...
2
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1answer
34 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 ...
3
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1answer
115 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 ...
1
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1answer
32 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 ...
0
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1answer
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
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1answer
71 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. ...
3
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1answer
114 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)....
5
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2answers
121 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 ...
4
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4answers
138 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: ...