Questions tagged [biomaterials]

Questions relating to biomaterials modeling.

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16 votes
1 answer
98 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 ...
Buck Thorn's user avatar
15 votes
1 answer
109 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 ...
Ivan's user avatar
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12 votes
1 answer
117 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 ...
mykd's user avatar
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12 votes
1 answer
1k 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 ...
BND's user avatar
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9 votes
1 answer
178 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 ...
Ivan's user avatar
  • 879
9 votes
1 answer
707 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 ...
Vranvs's user avatar
  • 423
7 votes
0 answers
140 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) ...
fred. vellieux's user avatar
6 votes
2 answers
2k views

How are diffusion coefficients calculated?

To support my laboratory result, I'm searching for an MD/statistical mechanics approach to predict translational diffusion coefficients in the liquid phase. I'm aiming to describe small peptides and ...
Giuseppe Basile's user avatar
5 votes
0 answers
104 views

Simulating a circuit diagram for action potential [closed]

Cable theory is a good simulation for the resting potential. It imagines patches of cell membrane lipid bilayer as capacitors and transmembrane ion channels as resistors. But it seems this model is ...
Always Confused's user avatar
5 votes
0 answers
43 views

How do I model drug diffusion from polymeric matrix? [closed]

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 ...
arun_kol's user avatar
4 votes
1 answer
69 views

Force field for charged peptide-ion system

I'm now currently simulating the system in which charged peptide (ARG, LYS, ASP, GLU) is solvated in electrolyte solution. MD simulation was performed based on the AMBER14ffSB force field, but in here ...
Arete's user avatar
  • 193
4 votes
1 answer
41 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.
Camps's user avatar
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4 votes
1 answer
68 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 ...
MarcelineH's user avatar
4 votes
2 answers
120 views

Non-Covalent Interaction between drug and DNA?

I am using classical molecular dynamics (MD) to observe a non-covalent interaction between my complex and the DNA, but there is a problem in that the complex interacts with the terminal of the DNA for ...
Abd-Elazeem Mohamed's user avatar
3 votes
1 answer
225 views

Convergence issues in DFTB+ calculations?

I am trying to calculate the Fermi level of a DNA-graphene system. I was able to get the calculations for graphene and DNA strand to converge separately. However, when I try to calculate the same for ...
Hemanth Haridas's user avatar
3 votes
1 answer
2k views

Why is the Alphafold PAE (predicted aligned error) not symmetric?

Cross-posted on AI Stack Exchange. We are running alphafold2 multimer on Google Colab to predict the association between two proteins. It generally works fine, but we get an asymmetric PAE plot for a ...
NKGon's user avatar
  • 31
3 votes
0 answers
38 views

How to select the best features for a drug discovery model? [closed]

I would like to build a regression model to predict a property of molecules not yet synthesized. I have calculated 5666 alvadesc descriptors for each SMILES in my experimental dataset, but comparing ...
vorsamaqoy's user avatar
2 votes
1 answer
142 views

How to control the thickness of lipid bilayer with GROMACS

I was trying to perform lipid bilayer MD for my protein based on GROMACS's Membrane Protein Tutorial. I can successfully orient the protein in the lipid (turquoise) as you can see in the image below: ...
littleworth's user avatar
  • 1,674
2 votes
0 answers
53 views

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

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"....
user4100's user avatar
1 vote
1 answer
105 views

What does "dynamics" mean in matter modeling?

As an example, I have seen the phrase "dynamics of proteins" or "dynamics of biomolecules". The review paper "Protein Dynamics" by J A McCammon has the word in its title, ...
user366312's user avatar
  • 2,392
0 votes
0 answers
43 views

Why is this geometry optimization in Gaussian not working for a system containing an amino acid, a water molecule and a metal (Pb) ion?

I started optimising a system containing amino acid residue, water molecule and a toxic metal ion, in proving a supposed reaction steps that might take place in inhibiting enzyme activity. The ...
PriZarah's user avatar
  • 309
-8 votes
2 answers
347 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?
Peter Morgan's user avatar
  • 1,473