15

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 :)


11

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 them following their functionality and extent of solvent exposure, what sites are suitable for occupancy by hydrophobic groups or by ligand hydrogen-bond donors,...


9

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 problem can be found here: Molecular Parity Violation and Chirality: The Asymmetry of Life and the Symmetry Violations in Physics, by Martin Quack. Another ...


6

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 that the electronic properties (charges and electrostatic potential surface) are directly related to the geometrical shape. Instead, they are related to the ...


6

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 ($R_g$) computation from a MD trajectory you commonly end up with a time series for the values for it, $R_g(t)$. From $R_g(t)$ you can already plot the time ...


4

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 is the ligand you are using to dock. The GLIDE software, for example, has been increasing the number of atoms and rotatable bonds it is able to handle. Since ...


4

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 academic use. If you need the system for molecular dynamics simulations, one can easily create input files, e.g. for NAMD.


3

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 article: T. Vampola, J. Horáček, V. Radolf, J. G. Švec, and A. Laukkanen, Influence of nasal cavities on voice quality: Computer simulations and experiments, J. ...


1

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 of each residue. So depending on the secondary structure, they may just alter how coarse the mapping is depending on how much detail is needed to emulate this ...


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