Ambit-Zwitterion: a Software Tool for Automatic Generation of Zwitterions
| Main Authors: | Kochev, Nikolay, Paskaleva, Vesselina, Jeliazkova, Nina |
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| Format: | info software |
| Bahasa: | eng |
| Terbitan: |
, 2018
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| Subjects: | |
| Online Access: |
https://zenodo.org/record/1481753 |
Daftar Isi:
- We present a new open source tool for automatic generation of all zwitterionic forms of a given organic compound. Ambit-Zwitterion is an extension of Ambit-Tautomer software, part of the open source software platform Ambit and developed on top of Chemistry Development Kit. All acidic centers in the target molecule (e.g. carboxylic groups, sulfonic groups, phosphoryl groups etc.) as well as all basic centers (e.g. amino groups) are preliminary identified. Ambit-Zwitterion implements a combinatorial algorithm for exhaustive generation of all zwitterions by making all combinations of k anions out of n acidic centers (Ck,n) and respectively all combinations of k cations out of m basic centers (Ck,m). Each combination from Ck,n anionic set is combined with each combination from Ck,m cationic set to generate all zwitterionic forms containing k zwitterionic pairs. All zwitterions are obtained by iterating k = 1,2,...,min(n,m). Zwitterion generation algorithm is customized by a set of configuration options. Ambit-Zwitterion is available as a command line application jar from this repository. Software example usage and test results with Drug Bank structure set are also presented. This work was supported by the Bulgarian National Science Fund under project “MolRobot” (DN0910/2016).
- Ambit link: http://ambit.sourceforge.net/ Ambit application examples: http://ideaconsult.github.com/apps-ambit (folder tautomer examples) Arginine tautomers are generated with ambit-tautomer (see http://ambit.sourceforge.net/ for more information)