Scopy
fixed mistake in ro5
Scopy （ Py ThonのS Crenning Co Mpounds）、初期の創薬で望ましくない化合物をスクリーニングするために設計された統合されたネガティブデザインPythonライブラリ。 Scopyには、データの準備、スクリーニングフィルター、足場と記述子の計算、視覚化分析をカバーする6つのモジュールが含まれます。
>>> conda install -c conda-forge rdkit
Scopyは、Python3環境の下でLinux、OSX、およびWindowsシステムで正常にテストされています。
>>> 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）ドキュメントのオンラインバージョンはこちらから入手できます：https：//scopy.iamkotori.com/
（2）クイックスタートの例：https：//scopy.iamkotori.com/user_guide.html
（3）アプリケーションの例（パイプライン）：https：//scopy.iamkotori.com/application.html
ご質問や提案がある場合は、[email protected]、および[email protected]にお問い合わせください。
このソフトウェアとその関連データとドキュメントをカバーする「MIT」ライセンスの詳細については、ファイルライセンスをご覧ください。
Yang Zy、Yang ZJ、Lu AP、Hou TJ、Cao DS。 Scopy：望ましいHTS/VSデータベース設計のための統合されたネガティブデザインPythonライブラリ[印刷前にオンラインで公開されています、2020年9月7日]。短いバイオインフォーム。 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},
}
私の同僚であるZiyiに感謝します。ドキュメントと記事の執筆を完了するのを支援してくれました。
