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Questions tagged [protein-structure]

The 3-dimensional organisation of amino acids in a protein, specifically including the secondary, tertiary and quaternary structures.

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Are there any primary structure sequences that strongly suggest b-sheet or alpha helix?

Is there a particular sequence of amino acids that we know will take on a beta-sheet or an alpha helix or is it essentially random?
user2879934's user avatar
11 votes
1 answer
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In which direction does ATP synthase rotate?

I heard about the rotation of ATP synthase in a biochemistry course. The professor said it will rotate counterclockwise. Is that true? If so, what mechanism defines its direction?
latra's user avatar
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Protein structure prediction from amino acids sequence

Information given at this resource https://predictioncenter.org/ is close to impossible to digest (as with everything in this field), so if anyone could tell me what is the accuracy we can predict ...
Taggart Comet's user avatar
8 votes
5 answers
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Examples of Differential equations in Biology

I am a mathematician currently teaching some math classes at a university. Next semester, I'll have bachelor's degree biochemistry students. I want to know where certain math tools might be needed in ...
Duarte Costa's user avatar
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4 answers
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Program (on Mac) to show 3D protein structures?

I have an assignment for 6th grade biology. I have to look at a 3D structure of a protein and manipulate it so it only shows the AA I’m interested in currently. what I already did I already looked up ...
BelgianCoder's user avatar
5 votes
2 answers
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Should there be separate Ramachandran plots for an amino acid in different contexts?

I understand the nomenclature of the phi and the psi angles of the alpha-Carbon atoms in protein stucture, but I am confused by the Ramachandran plot. Each alpha-Carbon atom (magenta) makes two ...
Polisetty's user avatar
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Why is ab initio protein secondary structure prediction less reliable than alternatives?

To predict secondary structure of proteins three types of Algorithms are used Ab initio, homology based and neural networks. Among these neural networks prove to be more accurate and give good results ...
katherinebridges's user avatar
3 votes
3 answers
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Why does it matter to predict protein structure?

And how do you predict it ? What is your input data (sequence of amino acids, temperature, pH, ...) ? Is there a "standardized" input that scientists agree on ? Moreover, I've read that knowing the ...
vlouve's user avatar
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Protein Structure Parameters

I'm wondering about the minimal set of parameters necessary to define a protein's structure. My understanding is that the backbone geometry is defined by the phi and psi angles (torsion angles), and ...
ZenPylon's user avatar
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3 votes
1 answer
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The meaning of the $\alpha$ helix and $\beta$ sheets in proteins [duplicate]

I asked this question to my Biology teacher and he, in collaboration with a Chemistry teacher, couldn't find the answer. My question is the following: "What does the $\alpha$ and $\beta$ represent in ...
Matt's user avatar
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Is there are theoretical limit to the number of proteins possible and their respective structure?

I saw an article saying that DeepMinds AI has catatogued every protein known to science. I guess "known to science" and what is the theoretical limit is not exactly the same thing but the ...
Sedumjoy's user avatar
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What is the length and number of the parts of a conformational epitope?

I am interested in the question whether exposure to protein A might create antibodies that also bind to protein B. I am wondering whether, if the antigen of protein A is a conformational epitope, it ...
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How similar do proteins have to be to trigger the same immune response?

The title really says it all. How precise or vague is the immunity we get from vaccination or from having encountered a germ before? Is it about protein parts that are recognised if they are ...
BlindKungFuMaster's user avatar
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1 answer
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Is the chitin in an insect's exoskeleton cross-linked?

This answer to the question How to clean and preserve a cicada's molted exoskeleton (exuvia)? states: The exuvia is made of cross-liked chitin, and will not decay. You don't need any special ...
uhoh's user avatar
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Simple protein graphics software for stick models

Anybody know of a good free molecular graphics system that allows PDB file input? I prefer that it does not use Java. I also prefer that it is online, although I would consider recommended software ...
TanMath's user avatar
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Does protein structure depend on phylogeny? [closed]

Proteins have two basic secondary structure forms - beta strand and alpha helix. Do these depend on the organism or do the two forms exist for every protein? For tertiary and quaternary structure: do ...
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