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

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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 ...
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93 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 ...
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165 views

RMSD during conformational transition in proteins

When I was investigating the differences between protein structures obtained by X-ray crystallography and NMR spectroscopy, I found the paper [1] compairing structures of several proteins resolved ...
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624 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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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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41 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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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 ...