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I am looking at the latest INCHI-1 software which supports molecules with 32 thousand atoms. I work with macro-molecules and want to use that to generate humongous InChIs. I've never used that INCHI-1 …

You have to convert the SMILES to a graph model. Most everything you want to do with SMILES requires you construct the graph model, i.e., nodes (atoms) and arcs (bonds). Once you have that, you can go …

I am wondering why there is the following inconsistency in InChI: penicillin G vs. penicillin G potassium salt uses the /p layer to drop a proton but chloramine-T vs. tosylchloramide drops an H from …

I personally find it educational (even cathartic) to type out my own SMILES and make my own resources to fit my own purpose. For example, I have written out all 20 amino acids in such a way that I cou …

This is a follow-up to my earlier question here How do I obtain a 3D MOLFILE for the lactose synthase structure, especially the catalytic center? about the lactate synthase. I am using the lactate syn …

You have to evaluate shortcomings as compared to something. You can make a list and say "but InChI doesn't represent X" where X is ranging around mixtures Markush groups polymers from repeat units …

I am desperately searching for an anabolic enzymatic reaction, ideally with a metal ion involved in the reaction complex, and for which -- unlike in the case of the lactose synthase -- we have snapsho …

How can we "draw" a coordination bond (dashed bond) in MOLFILE? I cannot find a bond property or option that would allow me to choose such a thing. So many drawings of organo-metallic compounds (e.g., …

So for example there is a paper by Ramakrishnan and Qasba which presents a model in a 3d stereo picture it has UDP-Gal, Glc, Mn++, a piece of the lactalbumin protein (?) and a piece of the lactose syn …

I am studying the 3D structure of the LDH from x-ray crystallographic imaging I was pointed to from Is there any stereospecific enzyme in PDB that catalyzes an anabolic reaction and has an entry showi …

I am going to post my own answer since now I have figured it out in much more detail based on the answer I had accepted above. I don't have the PDB file of the lactose synthase model above, but I was …