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Lazy File Reading with mmap
The example source code often provided with cheminformatics libraries to demonstrate the available functionality often try to address two conflicting requirements. On the one hand, these attempt to be...
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Ye cannae change the laws of physics
One of the problems with curating chemical databases of small organic molecules is filtering out bogus connection tables from legitimate molecules. One aspect of this challenge has been termed [Ed: “I”...
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Radioactivity — It’s in the air for you and me
Radioactivity, discovered by Madame Curie, is the process by which the nucleus of an “unstable” atom decays to a different form. As mentioned in a previous blog post, atoms are composed of protons,...
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Molecular Half-life: The light that burns twice as bright burns for half as long
In a previous post I described how to use cheminformatics to determine whether or not a compound was radioactive by checking for unstable atomic nuclei. Alas, such a binary yes-or-no classification is...
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Text Mining for a Worthy Cause
I recently received an e-mail from the charity “jeans for genes” introducing me to “black bone disease“, a rare genetic disease without a cure. It is more formally known as “Alkaptonuria” (OMIM entry)...
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On the other hand
The vast majority of amino acid residues that appear in peptides and proteins appear as their natural L-form enantiomer. This is the form of all amino acids as translated by the ribosome. However...
View ArticleExplicit and Implicit Hydrogens: Taking liberties with valence
The field of cheminformatics has two concepts of implicit vs. explicit when it comes to talking about hydrogen atoms. The first concept is at the internal data structure level where explicit hydrogens...
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On the other other hand
My earlier “On the other hand” blog post considered some of the issues of representing D- amino acids. In this post, I discuss the representation of amino acids with sidechain stereochemistry in...
View ArticleValidity checking antibody sequence data
NextMove Software’s Sugar & Splice product is a toolkit for handling biopolymers, including oligopeptides, oliogonucleotides and oligosaccharides (and combinations thereof). Amongst its many...
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How do I write thee? Let me count the ways
A recent posting to the CHMINF-L mailing list at the University of Indiana reiterates a point made by Steve Heller in his recent keynote address to the 2014 ICCS/GCC meeting in Noordwijkerhout. In that...
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