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The study of the molecular structure of biological macromolecules and how that structure relates to their function.

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Is there a reason for the lack of full RTK structures?

Bocharov et al. (2013) write that As there are no structures of full-length RTKs [receptor tyrosine kinases], we do not fully understand how different domains function together to mediate signal ...
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1answer
68 views

Why is the macromolecular composition of a human cell seemingly hard to find?

I am trying to find a 3D rendering or list of molecules by volume in a cell (originally I was searching for human, but I'll take any at this point!). I understand the open-endedness of the question: ...
3
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0answers
56 views

Automating figure-making with PyMOL

What I want to do I have a list of almost 200 PDB entries that I need to visually inspect. Luckily, the thumbnail image displayed on the PDB website (examples with RCSB or PDBe for a well-known ...
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0answers
12 views

Database of predicted protein-ligand binding/docking score

Is there a database of computationally determined "binding scores" across protein-ligand pairs in the PDB? My phrase "binding score" is deliberately generic, since any such score would be fine. In ...
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0answers
38 views

Comparison between banana and human dopa oxidase

Dopa oxidase - an enzyme which catalyses the conversion of L-dopa to dopachrome - can be extracted from bananas but is also present in the mamilliam brain as a precursor to a number of ...
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0answers
39 views

How does antibody structure relate to function? [closed]

I know that antibodies have 2 binding sites (as Y shape) so they can bind to 2 pathogens for agglutination. They have a hinge, heavy and light chains, constant and variable sections on these chains. ...
2
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3answers
92 views

What are the applications of predicting the structure of proteins?

Protein molecules are very important as they are used for catalyzing almost all the chemical reactions in the cell, regulation of gene activity and provide cellular structure. However, in predicting ...
3
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0answers
39 views

Why can polar molecules like water pass aquaporin better than unpolar like H2 or CO2

We learned in our lecutre, that aquaporin lets Water pass, but blocks Ions like H+ and unpolar molecules like CO2 and H2. The reasons for the Ion blocking are comprehensible, but I dont get, why less-...
3
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1answer
183 views

Why add hydrogens in molecular dynamics simulations?

In my molecular dynamics lecture, our prof said, that we always have to add hydrogen atoms to titratable groups, before we start the force field simulations, and that it is especially important for ...
3
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1answer
188 views

Parallel DNA double-helices with Watson–Crick base-pairing: Why do they not occur? [duplicate]

I know that parallel DNA helices exist and are governed by Hoogsten base pairing, but why can’t they be possible with Watson-Crick pairing? In the diagram below, if we were to flip one of the strands ...
2
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3answers
69 views

Why does sequence of amino acids presented on the Catalytic Site Atlas from a given protein differs from the sequence on the RSCB Protein Data Bank

I wanted to compare the amino acid sequence of enzymes for this project I'm working on and need to compare them at their catalytic site. For that, I went to the Catalitic Site Atlas to get the ...
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2answers
148 views

What are the structural factors affect enzyme's Km?

Is there any rules (should not be exact), to estimate the kinetic changes in an enzyme if I did any mutation on it? If I cannot estimate the new kinetic values, is it possible at least to clarify or ...
3
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0answers
43 views

What is the biggest structure in nature for structural coloration?

I'm interested in the actual sizes behind structural coloration: I find it fascinating and I think it may have a couple very nice applications. The problem is I couldn't find anything but vague ...
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3answers
3k views

Does any molecule other than DNA have a double-helical structure?

DNA is known to have a double-helical structure. Do any other molecules have this structure?
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2answers
1k views

How hard it is to determine a 3d structure of a protein?

I seeing tens of thousands of PDB files on the internet. I really want to determine a 3D structure of my protein of interest. I've heard that 3D structure determination is a complex, expensive, and ...
0
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0answers
31 views

Competitive binding with split GFP, YFP

My experiment uses YFP/GFP to monitor a protein-protein interactions and I am wondering, has there been any study done on species within a cell potentially interfering with the efficiency of the split ...
0
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1answer
287 views

What is meant by “complexity of carbon sources”?

My biology book states "life on earth depends upon carbon based molecules, most of these food sources are also carbon based. Depending upon the complexity of these carbon sources, different ...
5
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1answer
74 views

Generate mesh surface from protein structure

What tools are most widely used for generating a mesh surface of a protein from an x-ray crystallographic structure (from the PDB)? Pros and cons would be appreciated. I'd prefer the output to be a ...
6
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2answers
153 views

Are there functional examples of parallel DNA double helices?

The anti-parallel structure of the DNA double helix is well studied, but I am curious if there are any examples of parallel DNA double helices. There are reports of synthetic such structures; see this ...
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1answer
395 views

What does “local folding” means in secondary structure?

I'm new to biology field, so I'm learning all kinds of biochemistry knowledge for a bioinformatics project. I've found a few definitions of secondary structure online. For example, I found this brief ...
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1answer
60 views

At what point, when connected, do DNA strands become a helix?

When synthesizing DNA strands and beginning to "connect" them, how quickly does it become a helix? In this answer, canadianer says The helical structure is more stable than the "straight" form (...
6
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2answers
1k views

Twist in the DNA double-helix

DNA, has a deoxyribose sugar — phosphate backbone with the purine and pyrimidine bases, adenine, cytosine, thymine, and guanine connected to the deoxyribose sugar. (The base–sugar molecules are ...
11
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1answer
2k views

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?
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1answer
68 views

Subset of Protein Crystal Structures (from PDB)

Is there a well-accepted subset of the Protein Data Bank set of protein structures that: Has only "high quality" structures (may be differing metrics of this; e.g. resolution, size, or structural ...
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2answers
451 views

Does the Plasma Membrane have a hydrophilic interior/exterior/contain vesicles? [closed]

I am very new to the study of biology, and have been unable to find information in other sources which could tell me whether the plasma membrane has the following traits: has a hydrophilic interior ...
7
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1answer
99 views

Why does Thiamine pyrophosphate have phosphates?

The reactions that Thiamine Pyrophosphate(TPP) catalyses are associated with the thiazolium ring. Why is pyrophosphate a part of the structure of TPP then? What benefit do the additional phosphates ...
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0answers
75 views

Are sepals and petals analogous?

I came across a MCQ Question that asked sepals are analogous to petals or leaves?I think the answer is petals as both have same function of protection but different structures.Am I correct or the ...
3
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1answer
1k views

Why we utilize dextro glucose and levo amino acids?

Our body only digest dextro(Right handed) glucose and levo(Left handed) proteins and can't digest Levo glucose and dextro proteins. Why? Our body synthesis levo proteins. What is the reason?
3
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2answers
163 views

Sheep vs. Furry animals

Why can't we take the fur of a fox without killing or skinning it just like the sheep , what's the biological or chemical structure or even the trait which is on a sheep's body that separates wool ...
3
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0answers
86 views

Reduce protein structure representation dimensionality.

In my lab we are trying to extract spatial features from protein structures. The software we develop makes use of CUDA for all heavy number-lifting, thus we are limited by the GPU's memory (12GB). ...
6
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2answers
278 views

By just looking at an unlabeled picture, how do you know it is a protein?

I'm learning about proteins and need to understand this concept. What makes this colourful ball of squiggles identifiable? Why is it a protein, and not any other biomolecule (like DNA for example)? ...
4
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2answers
400 views

Which server to use for volume and accessible surface area calculation of proteins

I want to find the accessible surface area and the volume of a protein, giving PDB file as the input for the protein. I used two servers, 3vee and Vadar. For the PDB id, 1LTM, the websites are giving ...
2
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1answer
91 views

How to calculate the number of folds present in a protein [closed]

Suppose I have number of PDB files of proteins. How can I get the number of folds present in these proteins? Is the fold count derivable from the PDB files? If so, how?
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0answers
386 views

How to find the radius of gyration for a protein?

While going through the paper titled "GEOMETRIC ANALYSIS OF THE CONFORMATIONAL FEATURES OF PROTEIN STRUCTURES" by Manish Dutt, it talked about finding the radius of gyration of each protein structure. ...
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1answer
103 views

Biological significance of correlation between the radius of gyration and number of layers of convex hull of protein structure

While going through the paper titled "GEOMETRIC ANALYSIS OF THE CONFORMATIONAL FEATURES OF PROTEIN STRUCTURES" by Manish Dutt, I came to know that there is a correlation between the radius of gyration ...
1
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1answer
95 views

Rules of motif forming

I want to understand how a motif is present or not, can be deduced from a PDB file. Are there any rule of thumb for forming 3D motifs? Like a series of helices and sheets in some direction will lead ...
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2answers
635 views

How to find PDB id of an amino acid sequence

Suppose I have an amino acid sequence whose PDB id is unknown. Is there in online server that can find the PDB id of the corresponding amino acid sequence? is there any site that will find the pdb ...
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2answers
79 views

Server for protein structure prediction for multiple sequences

Does anybody have any idea about any online server that takes in multiple amino acid sequences in fasta format and outputs the 3D structure of the input amino acid sequences in the form of helix, ...
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0answers
66 views

How many residues can a reliable ab initio structural model contain?

A recent question on ab initio that I answered involved touching on the limitations of ab initio modelling. A review from 2009 put forward that typically only in the order of 100-110 residues could be ...
3
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1answer
906 views

How to perform a DNA structural alignment in pymol

How can I "fit" two DNA structures having different nucleotide sequences in PyMol? I would like to use the structure of a DNA-binding protein in PDB (1h9t), which is bound to DNA in the PDB file, ...
2
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1answer
974 views

Do drugs' levo isomers have a better interaction with the receptors in our body than dextro isomers?

Examples of levo drugs include levothyroxine, levocitrizine, and levodopa. Is there any specific reason why the receptors in our body exhibit this stereoisomerism and hold a high preference for the ...
2
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0answers
47 views

Can a stationary eye with a moving pupil exist? [closed]

I am making a sci-fi web-comic set on an alien world and I thought up an idea for an eye that works much like an eye from a mammal, but instead of moving the whole eye, only the pupil moves. This idea ...
0
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0answers
42 views

Normalise protein database domain-wise

Suppose we've collected a big (hundreds of thousands) library of different protein sequences with certain features. Then we want to use this data base to train a classifier. And for several ...
6
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2answers
23k views

Why is the DNA helix anti-parallel? [duplicate]

Why is it that DNA strands are running in anti-parallel fashion? Given the chemical base-pairing, they could have been parallel just as well.
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0answers
46 views

Can I explain the kinetics of a ligand looking at the ligand-protein co-structure?

Can I explain the kinetics of a ligand binding to a target protein (association and dissociation rates) by looking at the protein-ligand co-structure? Editing my question after a few comments: I ...
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0answers
36 views

Differences in structural target for LPS detection by LAL and MD-2/TLR4

I remember there being a significant difference in the pathogen-associated molecular patterns (PAMPs) used for detection of lipopolysaccharide (LPS) by mammalian cells and the Limulus amoebocyte ...
1
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1answer
90 views

What is internal symmetry in membrane proteins?

I have come across the term "internal symmetry" in the context of membrane proteins, but have never found a satisfactory definition. I'm struggling to figure out exactly what this term means... What ...
11
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1answer
3k views

What is the transmembrane 'Positive-Inside Rule' nowadays? Has the definition changed over time?

First definition. Two publications by von Heijne in 1989 and 1992 coined the 'Positive-Inside rule' and showed it's practical value in topology prediction of transmembrane helices. It was clearly ...
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1answer
99 views

Questions regarding a particular paper

With respect to the following paper: Automated identification of protein-ligand interaction features using Inductive Logic Programming: a hexose binding case study I have a few questions: in page 2,...
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0answers
298 views

Is the number of stamens always 9 for geranium?

We are studing in class the reproduction of plants. We start the lesson by observing some components of flowers, it was the Géranium. First of all we start counting the number of sepals , petals and ...