I select a series of CA atoms in a structure in pymol and show them as sphere in pymol and want to label them. If using the label menu at the up-right conner of pymol, the labels shown overlaps with spheres and can not be seen. So I wish to show the labels at a bit distance...
The TCR integrates forces in its triggering process upon interaction with pMHC. Force elicits TCR catch-slip bonds with strong pMHCs but slip-only bonds with weak pMHCs. We develop two models and apply them to analyze 55 datasets, demonstrating the models’ ability to quantitatively integrate and...
SDF files are formatted ASCII files that store information about the positions of the individual atoms (either in 2D or 3D space) that make up the molecule. The data on connectivity and hybridization state are also encoded, although their use is less frequent and often inconsistent. To browse,...
N6-methyladenosine (m6A) is a post-transcriptional modification that controls gene expression by recruiting proteins to RNA sites. The modification also slows biochemical processes through mechanisms that are not understood. Using temperature-dependent (20°C–65°C) NMR relaxation dispersion, we show t...
HETATM - coordinates of hetero-atoms. Related extensions: PDB files can also be saved asENTorBRK. Legacy: PDB is now considered a legacy format, being replaced by the newer mmCIF (extension:CIF) file format. Related associations: PDB could also refer to Microsoft's program database file - ...
How to extract your Ligand Select the chain of interest, go toActions ->Ribbon -> Hide. This removes the macro molecule. Now go toActions -> Atoms/Bonds -> Show. If you haven’t so already, now you are now able to see the ligand. Now go toActions -> Atoms/Bonds ->and choose ...
it's probably important to stop and think, as sometimes there is a reason there may not already be parameters for such atoms/clusters. In particular, here are a couple of basic questions you can ask yourself to see whether it's reasonable to develop/obtain standard parameters for these and...
We employ extensive all-atom molecular dynamics simulations to dissect the complete substrate exchange cycle of the bacterial NO3−/NO2− antiporter, NarK. We show that paired basic residues in the binding site prevent the closure of unbound protein and ensure the exchange of two substrates. ...
Oxygen atoms in TGN and TGC are shown in red. CETP is shown in gray cartoon. Full size image It is worth mentioning here that we could accommodate only the tuning fork conformation of TGs in the narrow tunnel of CETP. This is because TGs in tuning fork or chair conformation are thinner...
Here we show that AlbA binds albicidin with low nanomolar affinity resulting in full inhibition of its antibacterial activity. We report on the crystal structure of the drug-binding domain of AlbA (AlbAS) in complex with albicidin. Both α-helical repeat domains of AlbAS are required to ...