Questions tagged [biomaterials]
Questions relating to biomaterials modeling.
7
questions
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?
