Scopy
fixed mistake in ro5
Scopy ( S Crenning Co Mpounds в Py Thon), интегрированная библиотека Python с негативным дизайном, предназначенную для проверки нежелательных соединений в раннем обнаружении лекарств. Scopy включает в себя шесть модулей, охватывание подготовки данных , экранинг фильтров , расчет каркасов и дескрипторов , а также анализ визуализации .
>>> conda install -c conda-forge rdkit
Scopy была успешно протестирована на системах Linux, OSX и Windows под Enviloment Python3.
>>> git clone [email protected]:kotori-y/Scopy.git && cd scopy
>>> [sudo] python setup.py install
>>> conda install -c kotori_y scopy
>>> pip install scopy
(1) Онлайн -версия документации доступна здесь: https://scopy.iamkotori.com/
(2) Примеры быстрого начала: https://scopy.iamkotori.com/user_guide.html
(3) Примеры применения (трубопроводы): https://scopy.iamkotori.com/application.html
Если у вас есть вопросы или предложения, пожалуйста, свяжитесь с: [email protected] и [email protected].
Пожалуйста, смотрите лицензию на файл для получения подробной информации о лицензии «MIT», которая охватывает это программное обеспечение и связанные с ним данные и документы.
Ян Зи, Ян З.Дж., Лу А.П., Хоу Т.Дж., Цао Д.С. Scopy: интегрированная библиотека Python с негативным дизайном для желаемого дизайна базы данных HTS/VS [опубликовано в Интернете перед печати, 2020 сентября 7]. Краткая биоинформация . 2020; BBAA194. doi: 10.1093/bib/bbaa194
@article{10.1093/bib/bbaa194,
author = {Yang, Zi-Yi and Yang, Zhi-Jiang and Lu, Ai-Ping and Hou, Ting-Jun and Cao, Dong-Sheng},
title = "{Scopy: an integrated negative design python library for desirable HTS/VS database design}",
journal = {Briefings in Bioinformatics},
year = {2020},
month = {09},
abstract = "{High-throughput screening (HTS) and virtual screening (VS) have been widely used to identify potential hits from large chemical libraries. However, the frequent occurrence of ‘noisy compounds’ in the screened libraries, such as compounds with poor drug-likeness, poor selectivity or potential toxicity, has greatly weakened the enrichment capability of HTS and VS campaigns. Therefore, the development of comprehensive and credible tools to detect noisy compounds from chemical libraries is urgently needed in early stages of drug discovery.In this study, we developed a freely available integrated python library for negative design, called Scopy, which supports the functions of data preparation, calculation of descriptors, scaffolds and screening filters, and data visualization. The current version of Scopy can calculate 39 basic molecular properties, 3 comprehensive molecular evaluation scores, 2 types of molecular scaffolds, 6 types of substructure descriptors and 2 types of fingerprints. A number of important screening rules are also provided by Scopy, including 15 drug-likeness rules (13 drug-likeness rules and 2 building block rules), 8 frequent hitter rules (four assay interference substructure filters and four promiscuous compound substructure filters), and 11 toxicophore filters (five human-related toxicity substructure filters, three environment-related toxicity substructure filters and three comprehensive toxicity substructure filters). Moreover, this library supports four different visualization functions to help users to gain a better understanding of the screened data, including basic feature radar chart, feature-feature-related scatter diagram, functional group marker gram and cloud gram.Scopy provides a comprehensive Python package to filter out compounds with undesirable properties or substructures, which will benefit the design of high-quality chemical libraries for drug design and discovery. It is freely available at https://github.com/kotori-y/Scopy.}",
issn = {1477-4054},
doi = {10.1093/bib/bbaa194},
url = {https://doi.org/10.1093/bib/bbaa194},
note = {bbaa194},
eprint = {https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbaa194/33719387/bbaa194.pdf},
}
Спасибо моему коллеге, Ziyi, за то, что он помог мне завершить написание документа и статьи.
