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15 votes

How are quantum computers being used in drug design?

How are quantum computers being used in drug design? They are not. Because useful quantum computers do not exist yet. Ask again in a couple decades :)
Nike Dattani - No Free Time's user avatar
11 votes

Protein cavities - methodological starting point for basic characterization

The identification of cavities, for drug design, is beyond the geometric characterization (aka volume). The server and individual software, beside the geometrical cavity determination, characterize ...
Camps's user avatar
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9 votes
Accepted

Theoretical origins of stereochemistry

Relating to the question about electroweak chemistry: the parity violation effect of the weak force on chiral asymmetry has been considered for quite a while now. A good accessible introduction to the ...
Emil Zak's user avatar
  • 896
6 votes

How to characterize surface features in proteins?

Normally, if various proteins have the "same" cavities/clefts, this means that they are part of the same family and the amino acids that form the cavity are conserved. I really don't think ...
Camps's user avatar
  • 23.4k
6 votes
Accepted

How are diffusion coefficients calculated?

There are several different methods to calculate diffusion coefficients depending on the problem and some nuances to consider. Mean square displacement The most common way to calculate diffusion ...
WaterMolecule's user avatar
6 votes

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

It depends on your actual scenario. If we assume that you have two Molecular Dynamics (MD) replicas for the same protein (and their respective trajectories), then when you perform a Radius of Gyration ...
Ivan's user avatar
  • 879
5 votes
Accepted

Force field for charged peptide-ion system

If you are looking at the interactions between a charged peptide and ions, I would recommend that you look into polarizable FFs that are available in literature. I know that OPLS and CHARMM have ...
Hemanth Haridas's user avatar
4 votes

How are diffusion coefficients calculated?

I decided to make my comment an answer... Diffusion coefficients are simple to calculate in molecular dynamics. GROMACS has built in software specifically for this calculation. GROMACS diffusion ...
B. Kelly's user avatar
  • 4,366
4 votes

Is there a site to obtain or create membranes?

CHARMM-GUI It is possible to create molecular systems with a membrane using CHARMM-GUI. There is also a tutorial available. The current version requires a registered user account but it is free for ...
SLx64's user avatar
  • 141
4 votes

Docking proteins with glycans

The main issue here is not about the type of ligands (glycans) even when it is known that there are force fields that are specific for each type of system. The main issue is about how flexible and big ...
Camps's user avatar
  • 23.4k
3 votes

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

The paper bellow can give you some insides. Using a Computer Tomography recording, they build a 3D model for computer simulation using FEM (Finite Element Method) and then do a 3D printing. The ...
Camps's user avatar
  • 23.4k
2 votes
Accepted

Convergence issues in DFTB+ calculations?

I had posted the same question on the dftb+ forum and Prof. Aradi responded to the question with the following answer. A common strategy is for large metallic systems to start with a very high ...
Hemanth Haridas's user avatar
2 votes

Non-Covalent Interaction between drug and DNA?

Since it has been a month since OP agreed to write an answer without actually writing the answer, I will try answering this. The easiest way is to perform something called Enhanced Sampling ...
Hemanth Haridas's user avatar
2 votes

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

Predicted alignment error is not always symmetric. This page from the European Bioinformatics Institute says: "predicted_aligned_error: The PAE value of the ...
Nike Dattani - No Free Time's user avatar
2 votes

How to control the thickness of lipid bilayer with GROMACS

You can adjust the thickness of the water layer* by initialising your simulation with more or less water in it. The thickness of the lipid bilayer is determined by the types of lipids you use, and the ...
Shern Ren Tee's user avatar
2 votes

What does "dynamics" mean in matter modeling?

Unfortunately there's so many uses of the term "dynamics" that it can be hard for a beginner to figure out what it means, even if they're highly experienced in internet searches and ...
Nike Dattani - No Free Time's user avatar
1 vote

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

Thanks for updating the question PriZarah, I can now at least suggest what might be causing the problem. It's probably just very, very slow In your recent example, you are calculating a reasonably ...
leeman's user avatar
  • 246
1 vote
Accepted

What is the purpose of DSSP when using martinize2?

Just basically collecting the comments here. The tutorials page for Martini states: The secondary structure of the protein influences both the selected bead types and bond/angle/dihedral parameters ...

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