Scopy
fixed mistake in ro5
Scopy ( S Crenning COM MPOUNDS EM PY THON), uma biblioteca Python de design negativo integrado projetado para exibir compostos indesejáveis na descoberta precoce de medicamentos. A Scopy inclui seis módulos, cobrindo a preparação de dados , os filtros de triagem , o cálculo de andaimes e descritores e a análise de visualização .
>>> conda install -c conda-forge rdkit
A Scopy foi testada com sucesso nos sistemas Linux, OSX e Windows no Python3 Enviroment.
>>> 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) A versão on -line da documentação está disponível aqui: https://scopy.iamkotori.com/
(2) Exemplos rápidos de partida: https://scopy.iamkotori.com/user_guide.html
(3) Exemplos de aplicação (pipelines): https://scopy.iamkotori.com/application.html
Se você tiver dúvidas ou sugestões, entre em contato com: [email protected] e [email protected].
Consulte a licença do arquivo para obter detalhes sobre a licença "MIT" que cobre este software e seus dados e documentos associados.
Yang Zy, Yang ZJ, Lu AP, Hou TJ, Cao DS. Scopy: uma biblioteca Python negativa integrada para o design desejável do banco de dados HTS/VS [publicado on -line antes da impressão, 2020 7 de setembro]. Breve bioinform . 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},
}
Obrigado ao meu colega, Ziyi, por me ajudar a concluir a redação do documento e do artigo.
