7 votes

Tool for predicting interactions in the cell

You could try one of these tools to predict protein-protein interactions: Struct2Net Given two protein sequences, the structure-based interaction prediction technique threads these two sequences to ...
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  • 7,957
3 votes

Why is there a chloride ion in this 3D model?

It is a crystallisation artefact. Namely, the protein are placed in a condition where they fall out of solution without aggregating a gloop (as happens in most well in xstal trial) and to pack as a ...
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  • 3,434
2 votes

What are the standard ways to visualize protein-protein or gene-gene interactions?

Your list has two identifiers for the same node per line. In order to use it, you will need to change that. If you want to use the gene name (2nd and 4th fields, in your example), just run: ...
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  • 7,957
2 votes

Looking for a way to download all pdb files that detail a protein-drug complex

Proving a negative is hard, but to my knowledge I do not know a database that has all the structure of drug bound protein. I can give some close matches. First a few terms to be on the same page. A ...
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  • 3,434
2 votes

What are the standard ways to visualize protein-protein or gene-gene interactions?

since I am not yet allowed to comment, I will have to pots this as an answer. I guess Cytoscape (http://cytoscape.org/) would be a nice way to analyse such interaction lists/networks (still depends a ...
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  • 141
2 votes

Building network for biomarker interaction analysis

You can start by looking at the correlation (if data is non-parametric) of each variable with each variable of each data point you have. One thing that might change is the correlation between ...
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  • 4,622
2 votes

Tool for predicting interactions in the cell

IBIS reports protein interaction with other biomolecules. Your protein or homolog must exist in the Protein Data Bank. IBIS @ NCBI: https://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi "For a given ...
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  • 507
2 votes
Accepted

Running GSEA or comparable analysis with multiple variable interaction?

I'm not sure I understand "I would like to run GSEA or a similar analysis to find WGCNCA clusters that differ based on the interaction between the two main variables". I would run an ...
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1 vote
Accepted

Is it possible to predict protein-ligand binding kinetics using machine learning?

This is a comment to redirect to other answers, but go too long. Docking is the in silico prediction of where a ligand binds in a protein. There are several Q&As about docking here that are ...
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  • 3,434
1 vote

How to predict protein binding to ligands?

If you are training a machine learning algorithm you probably want to train against things you know to be true, rather than making predictions from the sequence and training against the predictions. ...
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  • 901
1 vote

finding RNA-protein physical interaction

If you were to treat the nucleotide like a ligand you could follow these steps on pymol, and find the measurements you desire. Calculating distances to centroids is a little bit more complex, as you ...
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  • 41
1 vote

Finding new drug-protein targets/interactions using a known one as base

If you have information on which part of the protein are interacting, and its sequence, you can search for homologous or similar sequences in other proteins. This would give you a list of potential ...
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  • 203
1 vote

Using signal peptide and the expression levels of signal recognition particle in secretome analysis

This is something that Qiagen's Ingenuity Pathway Analysis is meant to solve. Unfortunately, the process of solving pathway dependency problems like these is difficult, and frequently leads to the ...
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  • 11.5k
1 vote

What are the standard ways to visualize protein-protein or gene-gene interactions?

Several have mentioned the excellent Cytoscape desktop package for visualising interactions as a graph. If you want to build your own web-based visualisations (rather than using a pre-built website ...
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1 vote

What are the standard ways to visualize protein-protein or gene-gene interactions?

Usually interactions are represented in a graph, with edges representing the interactions (colors, thickness or values on the edges represent different properties of those edges). As far as I know, ...
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  • 4,622

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