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Questions tagged [protein-interaction]

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How to interpret the relationships of PTMs from BioGRID's data

On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file. I have several issues with this file. Foremost, I am not ...
user345394's user avatar
2 votes
0 answers
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What is the actual mechanism by which ApoA-1 Milano exhibits its phenotype?

ApoA-1Milano is a variant of the apolipoprotein A-I protein that was discovered by the University of Milan when sequencing the genome of those native to the village Limone sul Garda. The mutation has ...
小奥利奥's user avatar
2 votes
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What is the "GTP activator protein" that activates GTP-cyclohydrolase-1?

From GTP-cyclohydrolase deficiency responsive to sapropterin and 5-HTP supplementation: relief of treatment-refractory depression and suicidal behaviour (BMJ Case Reports, 2011) The metabolic profile ...
CopperKettle's user avatar
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2 votes
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functionality of protein based on amino acid covalently linked to something

This question is directly taken off from "challenge question" as part of my bio-engineering class. The functionality of any individual protein covalently linked to a device is dependent on the ...
Jason Kim's user avatar
2 votes
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String-db locally downloaded

I need a ppi network of cancer and it should have 200k to 300k proteins (nodes) As the web inteface don't allow more than 2000 ...
A M's user avatar
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2 votes
0 answers
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How to quantify the "stability" of a protein complex?

From experiment we've identified a subset of known mammalian protein complexes as interesting (approximately 50 CORUM complexes). We'd like to do an enrichment-style analysis to know more about them. ...
R Greg Stacey's user avatar
2 votes
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Interaction study of oligomeric proteins

I'm dealing with two different protein(say, protein_a and protein_b) which stays in an interacting-oligomeric form in biological system. I have so far successfully been able to purify both the ...
diffracteD's user avatar
2 votes
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What is the protein with the highest affinity to lactose?

I was wondering: What is the protein with the highest affinity to lactose? Are there some databases with values for affinity?
Pao's user avatar
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Should Secondary Antibody Bind better through adsorption than using an EDC Linker?

Recently, I conducted an experiment to compare the use of EDC versus passive adsorption. I attempted to immobilize goat anti-rabbit HRP secondary antibody to Carboxylated polystyrene beads via EDC ...
Matthew Huang's user avatar
1 vote
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What are the interaction energies/chemical potential values for the cytoplasm - protein interactions within the cytoplasm?

I'm trying to simulate phase separation in a biological based system using a Cahn Hilliard model. I have 3 components, they are 2 theoretical enzymes and the cytoplasm. I have found plenty of sources ...
JollyBioComputer's user avatar
1 vote
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Peak-calling in CLIP: What is the effect of RNA-concentration?

I hope it's ok to repost my question from 8 months ago from StackExchange:Bioinformatics, that is still in beta. https://bioinformatics.stackexchange.com/questions/10730/peak-calling-in-clip-what-is-...
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Get Network Out of proteins of interest

I have generated a list of Proteins using oncogeenes and suppressor genes of cancer. I have 5827 mapping identifier for 3916 interactions using STRINGdb R package . How do I build a network of 200k ...
A M's user avatar
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1 vote
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Biogrid interaction protein network

I need a ppi network for cancer or Alzheimer . I'm using BioGrid , In the search field I can specify the gene id only , I want to know how can I make an interaction network for one of the disease ? ...
A M's user avatar
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1 vote
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map list of proteins into an already built network

I have a built reliable network which can be downloaded from here http://www.filedropper.com/mynetwork This network is bulit using Cytoscape. Now I have a list of proteins IDs, for example ...
Nik's user avatar
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1 vote
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What are the structural characteristics of a protein-protein interaction network

I am an researcher in computer science. I am interesting in the alignment problem of PPI networks of difference species. I know a PPI network is a graph in its nature. I want to know whether there are ...
Saturn's user avatar
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If species are reproductively isolated, then how are interspecific hybridisations carried out?

during fertilisation there is compatibility test done so that both sperms and eggs are of same species. the zona pellucida of egg bears sperm specific receptor proteins(ZP3 receptor proteins) which ...
Pearl Dua's user avatar
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1 answer
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What tools can help me determine if a plant homologous protein interacts with an ncRNA in the same way?

First post here, so bare with me if I violate any etiquette or formatting rules. Let's say I've got a protein in humans. When it interacts with an ncRNA found in humans, it does something that I'm ...
Christopher Hendrickson's user avatar
-1 votes
1 answer
190 views

Stringdb using R Bioconductor package

I need to retreive a large dataset from String-db. I 'm newbie in R so even with the documentation , I could not get the dataset fron String How do I do to retreive a network from String 2k to 3k ...
A M's user avatar
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