The process in which a protein folds into a three-dimensional shape to achieve proper functioning.

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1answer
69 views

Is using Hidden Markov Models to find homologues sensible in abstract, short sequences?

HMM alignment tools like hhpred excel at finding subtle homologues of folded proteins that simpler scoring techniques (such those used in BLAST algorithms) would miss. I am only looking at a small ...
3
votes
0answers
79 views

Experimental techniques to measure protein-protein and protein-ligand structure and dynamics

We would like to compare our simulation results with experimentation. When one wants to follow experimentally the dynamics (and possibly structure) of protein-protein or protein-ligand docking ...
2
votes
0answers
24 views

Is it possible to isolate and analyse intermediates of protein folding?

I would like to know if there is an assay which could allow us to analyse a protein before it has assumed its 3D functional form. While studying structural biology, I only came to know the forces that ...
2
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0answers
20 views

Protein Design - Target Structure Specification

I'm curious about how protein structures are defined in general, but in particular, I'm wondering how a target structure can be specified without knowing the amino acid sequence. For example, in ...
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0answers
22 views

Incremental denaturation of protein mixtures

When a protein solution is heated above the denaturation temperature, it seems that denaturation does not happen at the time the temperature is reached, but it takes some time. I assumed that ...
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0answers
19 views

Protein secondary structure prediction

I'm trying to predict the protein secondary and 3-D structure for the sequence [Q1NN20] and need some help getting the ball rolling. I'm getting confused with how and when to use Jpred, swiss-mod, ...