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12 votes
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Is tyrosine hydrophobic or hydrophilic?

The answer to this question emerges from an examination of the structure of tyrosine — or, more strictly, the tyrosyl residue, which is how it exists in proteins, the concern of the question: It ...
David's user avatar
  • 26.2k
8 votes
Accepted

Where can I find large datasets of protein-interaction networks?

There is a bunch of decent protein-protein interaction databases: Biocarta, BioGrid, DIP, InnateDB, IntAct, MINT, PPID. Some of them aren't available now, but you can download datasets from the ...
Maxim Kuleshov's user avatar
4 votes

Is tyrosine hydrophobic or hydrophilic?

Tyrosine (Tyr or Y, 4-hydroxyphenilalanin) is usually reffered as polar amino acid because its hydroxyl groupe (polar is rather hydrophilic), but there is a catch with the benzen ring and stacking pi-...
Lukien Chumi's user avatar
4 votes
Accepted

What are " temporal kinetics"?

Temporal kinetics does not refer to the kinetics of kinase phosphorylation reactions and, since it is not standard terminology, you likely wouldn’t find its meaning in any textbook. The authors of the ...
canadianer's user avatar
  • 17.8k
3 votes

How does one derive a KD from an equilibrium titration experiment?

The models you are using are based on the Langmuir Isotherm. The classical use of this model is for gas adsorption to a solid. In these experiments, the pressure of the gas is measured against the ...
stords's user avatar
  • 967
3 votes
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Application of molecular dynamics simulation (or alternatives) for the full pathways of protein interactions?

MD is used for studying structural changes. Simulation of biochemical pathways involves the kinetics (you are not really looking at how enzyme structure changes when it binds to substrate). You can ...
WYSIWYG's user avatar
  • 35.6k
3 votes

How does the order of the pairs of cross-links in DNA determine the arrangement of the amino acids?

Yes, it was solved in the early 1960s, starting about 1961. See Wikipedia's Genetic Code - History, and perhaps "Establishing the Triplet Nature of the Genetic Code".
mgkrebbs's user avatar
  • 9,073
3 votes

Is there an enzyme that functions without being associated with a complex?

Acetylcholinesterase. Chosen because the esterase seems like a low energy reaction so it wouldn't need energetic co-factors. https://en.wikipedia.org/wiki/Acetylcholinesterase Not sure if I should do ...
Polypipe Wrangler's user avatar
3 votes
Accepted

Why bovine serum albumin is used in mass-spectroscopy and how to interpret such data?

Their LC-MS-MS data was only semi-quantitative as gathered, meaning they could compare relative levels of one protein to another in the same sample, but not necessarily between different samples with ...
MattDMo's user avatar
  • 15.3k
3 votes

How does the body detect irreversible binding to receptors?

The process of downregulating a receptor by internalizing and degrading it in response to (sometimes prolonged) activation or (sometimes prolonged) failure to activate is what pharmacologists call ...
De Novo's user avatar
  • 8,811
2 votes

Will the interaction of two proteins vary across different tissues?

Your example of an interaction mediated by a scaffold protein is certainly one way of controlling protein interactions. This doesn't just happen in different tissues either, it is also used to fine-...
Nicolai's user avatar
  • 4,391
2 votes
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Query regarding KEGG KGML pathway files

See the manual: PPrel, in each of these, means protein-protein interaction, so we want to approach these by thinking about what the protein products of these genes can do with eachother. For the ...
De Novo's user avatar
  • 8,811
2 votes

Binding BSA to silver surface via large difference in isoelectric points of the two materials

Concerning the apparent discrepancy between your first and second citations, the difference in values is addressed by the authors in the more recent work: Perusal of the literature yields few IEP ...
acvill's user avatar
  • 8,296
2 votes
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Do RNA modification proteins bind to specific repeats on the RNA polymerase II CTD?

In attempting to answer questions about protein structure, the first port of call (which one might expect the questioner to have also visited) is the Protein Data Bank — the global repository of such ...
David's user avatar
  • 26.2k
2 votes

How many proteins could participate in a complex

The problem with coming into bioinformatics from a non-biological background is all too apparent in your question, and very real. You are dealing with a category of object called a protein complex, ...
David's user avatar
  • 26.2k
2 votes

Computational approaches for making hypotheses about the effects of genetic engineering? Experiment planning methods?

I suspect that what you are asking for is years in the future yet. Bear in mind that the use of CRISPR-CAS9 is just entering clinical trials for a very few, well studied diseases. Almost all the work ...
Charles E. Grant's user avatar
1 vote
Accepted

How does HIV assemble its capsid correctly?

How capsids self-assemble isn't fully known for any virus, but it's been studied a lot and there are a number of principles we can apply. First, HIV isn't as unique as you assume. 30 is a fairly large ...
timeskull's user avatar
  • 3,939
1 vote

Where would vegetarians/vegans get a substitute of hemo/myoglobin from?

The following informations is taken this source. It also lists some references. If this doesn't answer your question let me know in the comments. Iron is found in food in two forms, heme and non-heme ...
Science123's user avatar
1 vote

Fluorescent protein tags and colocalisation

"Are protein A and B co-located?" The answer is that it depends. Since your test question included the word "necessarily", this means that the answer to the test question is no. All you have to do is ...
tel's user avatar
  • 3,781
1 vote

False positives in TAP - MS experiments

The common repository for affinity purification (CRAPome) contains the results from many tandem affinity experiments and scores them based on their presence in control purifications. The database can ...
Michael_A's user avatar
  • 1,305
1 vote

Biological validation of computationally determined gene-gene interaction

I'm gonna try to cover as many scenarios as I can think of: Gene interaction ( = co-expression): This is probably the easiest to validated (e.g. by western blot like you mentioned) but the hardest to ...
Nicolai's user avatar
  • 4,391
1 vote

Biological validation of computationally determined gene-gene interaction

Hang in there, this answer will grow over time. Just off the top of my head, I think we could write a small book (or a very long review article) to cover both the depth and the breadth of your ...
mdperry's user avatar
  • 3,527
1 vote
Accepted

What are the types of interactions in biological network (protein networks)?

Most of them are pretty self-explanatory. KEGG pathways are often vague, as a lot of the specific biology for some proteins has yet to be properly investigated - sometimes you only know that two ...
Jared Andrews's user avatar
1 vote

What's the difference between physical (direct) and functional (indirect) protein interaction?

As I understand it, "physical" and "functional" are just two different ways of analyzing an interaction between proteins. Proteins can and do interact physically, meaning they can bind in specific ...
Filipe Rocha's user avatar
1 vote
Accepted

Rules of motif forming

A motif is a pattern that you discover in a structure by analysis. For example, common sequence motifs are short sequence fragments with parts similar to a regular expression. So, if you have a motif ...
gilleain's user avatar
  • 890
1 vote

How would one determine if an up regulation of one protein leads to an over expression of another?

To demonstrate a causal relationship where protein A leads to increase in protein B, you need to experimentally increase the level of A and measure if B increases. Over-expression is typically done ...
Roland's user avatar
  • 5,725
1 vote
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difference between motifs, domains, patterns, signatures and profiles

Looking at the documentation you provide, I think that I can provide definitions for those terms as defined by EXPASY. Note that those definitions may just be an in-house system that EXPASY uses that ...
Maximilian Press's user avatar
1 vote

How do prions transmit their conformation to other proteins?

It is thought that infectious prions exist as clusters forming a crystalline structure. When a protein with the same primary structure is encountered but with a different tertiary structure, the ...
Graham Chiu's user avatar
1 vote

Protein-protein interactions search

You can try to use IntAct Molecular Interaction Database. The data in this database is based on: data from the literature or from direct data depositions by expert curators <300k binary ...
KingBoomie's user avatar
  • 2,390

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