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

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33 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 ...
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1answer
69 views

Is there a way to see what representations are currently displayed in PyMOL?

I am using PyMol to visualize .pdb protein structures. I show/hide representation a lot, and sometimes I get confused with what representations are currently displayed. So I end up with doing a lot ...
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1answer
6k views

Why do the major and minor groove exist in DNA?

So I know that the major/minor groove arise from the offset pairing of the two strands in the helix. All my textbook tells me is that "pitch causes the off-set pairing of DNA and this gives rise to ...
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1answer
53 views

Where can I find pdb files for macromolecules like receptors?

I have tried going to the RCSB website and quite frankly it was useless since when I looked up receptors like say the metabotropic glutamate receptor 2 (mGluR2) I got no helpful results.
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18 views

How does the shape of the structure explain the function of that structure in both plant animal cells? [closed]

Could some please tell me how the structure explain the function of something in plant and animal cells, it is in middle school level.
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38 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
20 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 ...
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29 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 ...
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589 views

How can the directionality of a protein structure be defined?

For a DNA molecule, you can define directionality using the convention of a 5'-3' direction on the Sense strand. However, using an N to C convention for a protein doesn't work since the ends may be on ...
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40 views

Visualizing secondary RNA structure binding to target

I am designing synthetic ribozymes, and need to see the secondary structure that arises from its flanking arms binding to a target mRNA. I've used Mfold as well as IDT's OligoAnalyzer (Hairpin), but ...
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1answer
44 views

About molecules and their shape

When a molecule is being used in some biochemical process it has a certain 3-d structure. Is this maintained throughout it's usage or can one specific molecule change it's 3-d shape while it is being ...
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12 views

What is the most widely understood phrase that distinguishes “internal coordinates” from other non-Cartesian coordinates?

In structural biology, the phrase "internal coordinates" is usually understood as a spherical coordinate system consisting of bond lengths, bond angles -- determined from 3 atoms and given as internal ...
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30 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 ...
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12 views

Biomolecule , DNA-RNA difference [duplicate]

Why is that a RNA has uracil in place of thymine? RNA could have thymine bases but it has uracil ? What is the reason for the presence of uracil there ?
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1answer
98 views

Using Jpred to predict secondary structure

I'm trying to use Jpred to predict secondary structure for a protein sequence. When I run J-pred, I get a bunch of hits from PDB. I've also noticed these 'hits' are the same name as the templates i ...