curation-computational-chemical-libraries-demonstrated-with-alpha

Curation of Computational Chemical Libraries Demonstrated with Alpha-Amino Acids

Exhaustive generation of molecular structures has numerous chemical and biochemical applications such as drug design, molecular database construction, ...

Friedrich-Schiller University

The generation of constitutional isomer chemical spaces has been a subject of cheminformatics since the early 1960s, with applications in structure elucidation and elsewhere. In order to perform such a generation efficiently, exhaustively and isomorphism-free, the structure generator needs to ensure the building of canonical graphs already during the generation step and not by subsequent filtering. Here we present MAYGEN, an open-source, pure-Java development of a constitutional isomer molecular generator. The principles of MAYGEN's architecture and algorithm are outlined and the software is benchmarked in single-threaded mode against the state-of-the-art, but closed-source solution MOLGEN, as well as against the best open-source solution PMG. Based on the benchmarking, MAYGEN is on average 47 times faster than PMG and on average three times slower than MOLGEN in performance.

Mehmet Aziz Yirik

Biography

JoVE Journal Publications

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