Natural Product Database, 可用于筛选潜在有效的天然活性成分, 或者识别药材中潜在的成分.
ZINC12 库子集
ZINC含有多个子集, 更多可以根据目录来查看更合适. 其中和天然产物相关的子集是ZINC Natural Product Database (ZNP), 这里面包含了11个库. 这些库经历了一些过滤 (过滤规则, 如天然产物分子量大于600会被过滤). 这些库包括:
- TCM Database@Taiwan, 著名的最大收录中药成分的免费数据库
- Herbal Ingredients In-Vivo Metabolism (HIM), 同济大学的中药体内代谢物库, 较小.
- Herbal Ingredients Targets, 草药成分和靶点数据库 (HIT)
| Name | Last Updated | Vendor Catalog Size | ZINC Entries | Filtered | Unique |
|---|---|---|---|---|---|
| IBScreen NP | 2015/6/21 | 56799 | 84215 | 6199 | 7030 |
| TCM Database @ Taiwan | 2014/1/31 | 57423 | 36043 | 13698 | 675 |
| AnalytiCon Discovery NP | 2013/2/17 | 5154 | 11247 | 684 | 4549 |
| Specs Natural Products | 2015/11/23 | 880 | 1489 | 8 | 510 |
| NPACT Database | 2013/9/17 | 1574 | 1423 | 93 | 36 |
| AfroDb Natural Products | 2013/11/5 | 954 | 885 | 7 | 745 |
| Herbal Ingredients Targets | 2013/8/12 | 531 | 802 | 23 | 64 |
| Herbal Ingredients In-Vivo Metabolism | 2013/8/12 | 1270 | 663 | 61 | 27 |
| Nubbe Natural Products | 2013/1/28 | 643 | 588 | 19 | 22 |
| UEFS Natural Products | 2011/11/29 | 503 | 473 | 7 | 382 |
| Indofine Natural Products | 2013/2/18 | 64 | 144 | 2 | 30 |
ZINC15 库子集
ZINC15子集内包含有多个子库, 其中和天然产物相关的有几个:
- biogenic, 代谢物和天然产物库
- np-derived, 是天然产物的衍生化合物
- endogenous, 人源内源的代谢物库
- metabolite, 各物质的初级代谢产物库.
| short_name | name | Count | updated |
|---|---|---|---|
| tcmnp | TCM Database @ Taiwan | 37709 | 2015/9/1 |
| uefsnp | UEFS Natural Products | 510 | 2016/3/3 |
| msnp | MicroSource Natural Products | None | 2015/9/1 |
| himnp | Herbal Ingredients In-Vivo Metabolism | 1648 | 2015/9/1 |
| hitnp | Herbal Ingredients Targets | 774 | 2015/9/1 |
| npactnp | NPACT Database | 1545 | 2016/2/29 |
| afronp | AfroDb Natural Products | 880 | 2015/9/1 |
| indofinenp | Indofine Natural Products | 113 | 2016/10/31 |
| acdiscnd | AnalytiCon Discovery Natural Derivatives | 27886 | 2018/11/28 |
| acdiscnpbb | AnalytiCon Discovery NP BB | 241 | 2018/11/28 |
| acdiscnp | AnalytiCon Discovery NP | 11839 | 2018/11/28 |
| molportnp | MolPort Natural Products | 170600 | 2018/8/29 |
| specsnp | Specs Natural Products | 2121 | 2018/9/11 |
| asternp | Aster Sunflower family NP | 2612 | 2016/11/14 |
| hmdbtoxin | HMDB Toxin | 708 | 2017/8/17 |
| biopurify | Biopurify Phytochemicals | 2715 | 2018/9/27 |
| timtecnd | TimTec Natural Derivatives | 4942 | 2018/9/17 |
| nubbenp | Nubbe Natural Products | 2712 | 2017/8/17 |
其中, MicroSource Natural Products, AnalytiCon Discovery Natural Derivatives, AnalytiCon Discovery NP BB, MolPort Natural Products, Aster Sunflower family NP, HMDB Toxin, TimTec Natural Derivatives, Biopurify Phytochemicals是之前没有收录的.
TCM Database@Taiwan
在Non-duplicate可以下载到以下两个非重复的内容:
- 化合物数据库: 解压后有60563个化合物, 名字比较奇怪, mol2格式.
-
Natural product compounds obtained from ZINC, 下载解压后是1G的
zinc_natural.sdf: 194116个ZINC记录,共225667个分子 (2019.1.8)
中国天然产物化学成分库
中国天然产物化学成分库 国内一个不错的数据库, 收录了约1万多种化学成分, 包括了中文名, 英文名. 分子式分子量等.
Reference
- Data Resources for the Computer-Guided Discovery of Bioactive Natural Products, DOI: 10.1021/acs.jcim.7b00341
- Characterization of the Chemical Space of Known and Readily Obtainable Natural Products, DOI: 10.1021/acs.jcim.8b00302
- TCM@Taiwan : TCM Database@Taiwan: The World's Largest Traditional Chinese Medicine Database for Drug Screening In Silico
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