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

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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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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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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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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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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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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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Material with very small young's modulus [on hold]

I'm looking for a material with a Young's modulus of less than 100 Pa. I've looked at elastomers, but I haven't had any luck. Thanks for your help, I appreciate it.
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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 ...