Questions tagged [biomaterials]

Questions relating to biomaterials modeling.

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3
votes
1answer
38 views

Is there a site to obtain or create membranes?

I am interested in creating an enterocyte intestinal basal membrane. So, I wonder if there is a database or site where the membrane could be downloaded or created.
5
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0answers
31 views

How do I model drug diffusion from polymeric matrix?

I have been redirected to this forum from Chemistry SE. My problem consists of a structure (say a cylinder) made from a homogenous distribution of a drug from a polymeric matrix. These compounds are ...
2
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0answers
38 views

Chemical Structure of Iron Manganese Silicate Nanoparticle (IMSN) Nanozyme?

Hope you're doing well. Actually I am working on a project related to DNA regulated Nanozyme and I have a nanozyme of mesoporous silica "Iron Manganese Silicate nanoparticle (IMSN) nanozyme"....
9
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0answers
85 views

What is the purpose of DSSP when using martinize2?

I am studying an IDP with a lot of helical secondary structure, and trying to find a trajectory that I can use as an ensemble that fits my SAXS data. My starting models are the output from the Robetta ...
4
votes
1answer
62 views

Has there been any work done on fluid dynamic or acoustic modeling of the human oral (or nasal) cavity?

The purpose is for me to develop a deeper understanding of speech production and how distinct features that identify a phenome are produced. ab initio models based on classical & statistical ...
12
votes
1answer
126 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 ...
9
votes
1answer
71 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
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0answers
102 views

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

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) ...
12
votes
1answer
96 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 ...
15
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1answer
90 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 ...
16
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1answer
76 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 ...
-8
votes
2answers
220 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?