Questions tagged [biomaterials]

Questions relating to biomaterials modeling.

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8
votes
0answers
42 views

How much of a difference in a protein's radius of gyration can be considered significant?

In molecular dynamics simulations of proteins, the radius of gyration is often used to assess the compactness of a protein. When comparing two protein radius of gyration, what difference can be ...
7
votes
0answers
35 views

Docking proteins with glycans

Do you know of a good software or web server tool that helps doing docking of proteins with rather large glycans? An example I'm interested in is tens of dimers of sugars (or similar), docked to ...
7
votes
0answers
80 views

How to do molecular dynamics calculations and analyse trajectories of small molecules?

I need to perform some MD calculations and then trajectories of some small molecules analyzed. What I have is protein cofactor (FAD) small molecule (either single O2 molecule or single Chlorine atom) ...
11
votes
1answer
85 views

Theoretical origins of stereochemistry

What are the current theories of computational chemistry for studying homochirality (for example the phenomenon discussed here, here and in many other places)? Electroweak chemistry has been developed ...
14
votes
1answer
76 views

How to characterize surface features in proteins?

When looking at the structure of protein domains I notice many of them show a cleft-like structure in the same location (when aligned to each other). What is a recommended way of characterizing these ...
15
votes
1answer
62 views

Protein cavities - methodological starting point for basic characterization

Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest ...
-6
votes
2answers
154 views

How are quantum computers being used in drug design? [closed]

A biomaterials question this time. How are quantum computers being used in drug discovery and design?