Structural Classification of Proteins database Puns

Hi, I'm a computational structural biologist starting to look into the geometry of ionic bonds as they exist in proteins. I'm a computer scientist and not chemically trained (at least not formally), so please forgive me for the probable lack of depth in my question.

I would like to be able to detect the positions of ionic bonds as they exist in protein structures, based on an analysis of atomic coordinates and their distances from each other.

Generally, the information I've been able to find in a textbook (Lehninger biochemistry) and online (various) is too high level to be useful. These sources comment that protein ionic bonds occur between the side chains of amino acids with opposite net charges. That isn't enough information for me: I need to know exactly how far specific atoms of a negative amino acid (say, glutamate) need to be from specific atoms of another amino acid (say, arginine), to be considered an ionic bond.

I realize that proteins are dynamic, flexible objects and that accommodations must be made for that. However, I'm only interested in the analysis of static structures for now, and I just want to be able to say if an ionic bond exists, instantaneously, in a given structure.

A point of possible confusion here is that an ionic bond, as I understand it (and it's entirely possible that I misunderstand) is often obfuscated with an electrostatic interaction. I get that Coulombic forces attract these amino acids, but Coulombic forces apply at any distance, so they dont define a bond. As far as I understand, there must be a distance cutoff beyond which we no longer call such interactions "ionic bonds".

It is surprising to me that information about hydrogen bonds is much better defined. You have atoms named a donor, a donor hydrogen, an acceptor, and an acceptor antecedant, and they must satisfy certain distances and angles to be considered a hydrogen bond. It is super easy to write some simple code to detect them. I'd like to be able to do the same with ionic bonds, but I cannot find clarity. I presume I'm looking in the wrong places, or too clueless to see it staring me in the face.

There may be something with ionic bonds that defies this kind of clarity, and if so, please explain. I am all ears. Even if you don't know, I'd be very grateful if you can point me to an authoritative source, where I can look. Whatever the final answer, I need that authoritative citation anyways.

Hello fellow labrats,

I'm trying to find out if our human cell line expresses a protein (and the levels, if available) before transfection and I'm not sure how to go about looking for that information. Wondering if any of you have ideas.

I know about CCLE but that's for gene expression and also somehow didn't find my protein (gene) of interest there for our cell line.

Thanks.

Here is Github documentation from Children's National Health System project, Bionano solved this issue that customers facing with acquisition of BioDiscovery. BNGO management is really building complete solution. here is link to github project

https://github.com/VilainLab/nanotatoR

https://preview.redd.it/nyec034pmnz71.png?width=1098&format=png&auto=webp&s=db382acc2c03e1bc4e0447ee8a1eaee93704cc26

I'm wondering if anyone knows of any useful databases or resources where I can look at 3D protein structures of viral epitopes and compare/contrast changes in structure after amino acid changes that could impact subsequent TCR binding (ie via steric hindrance or otherwise)?