Re: [Rdkit-discuss] Cheminformatics Graduate School Recommendations?

[cmayerb1]

Patrick,

 

I’m not aware of any graduate programs specifically for cheminformatics (others 
may have more knowledge or experience in this area).  If you have specific 
schools in mind, check out the research areas of the chem faculty; usually 
you’ll find 1 or 2 with interests that overlap with cheminformatics research.  
That’s how it worked for my M.S. (Rutgers University-Camden), at least.  
Biology departments might be worth a try, either on a molecular scale (e.g. 
conformational screening of protein ligands) or population scale (e.g. 
comparisons among several environmentally toxic compounds that could suggest a 
mechanism of toxicity).

 

Hope the grad school search goes well!

-Chris

 

From: Patrick Neal  
Sent: Monday, July 19, 2021 12:15 PM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] Cheminformatics Graduate School Recommendations?

 

Hi All,

I apologize if this is too far off topic, but I got a recommendation to ask 
here since this community is the most likely to know!

I'm about to graduate from my undergrad chemistry program and I'm looking for 
graduate schools. I started in traditional computational chemistry research, 
but have really loved the cheminformatics/datascience aspects of drug 
discovery. I'm hoping to ask the community if you all have any recommendations 
for academic labs (ideally US based) with interesting cheminformatics research?

I'm specifically interested in fingerprinting methods (encoding 
3D/conformational information), similarity search/clustering compounds at 
scale, and automation tools for QM calculations. But, I would be grateful to 
hear of any labs you think are doing great cheminformatics work!

All the best,

Patrick

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[Rdkit-discuss] finding atoms at multiple bond distances from target

[cmayerb1]

Good morning,

 

I'm familiar with the atom.GetNeighbors() function to find all atoms within
one bond distance of a given atom.  Is there any method (either built-in or
user-created) to find all atoms within n bond distances (n >= 2) of a given
atom?  I'm working on a method to assign relative stereochemistry (D or L)
to alpha-amino acids, which (to my first estimation) depends on the atomic
numbers of the sidechain atoms within the first 2 bond distances of the
alpha-carbon.  I'm currently iterating through the sidechain atoms after
identifying the backbone heavy atoms (alpha-nitrogen, alpha-carbon, and
carboxylate carbon), and am curious if there is some way to simplify this
process by getting a list of atoms at progressively larger bond distances
from a specific atom.

 

Thanks for your time, any advice is welcome.

 

-Chris

 

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