ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery.
ZINC20-A Free Ultralarge-Scale Chemical Database for Ligand Discovery.
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DOI：
10.1021/acs.jcim.0c00675
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发表时间：
2020-12-28
影响因子：
5.6
通讯作者：
Sayle RA
中科院分区：
文献类型：
--
作者：
Irwin JJ;Tang KG;Young J;Dandarchuluun C;Wong BR;Khurelbaatar M;Moroz YS;Mayfield J;Sayle RA
识别和购买新的小分子以在生物测定中进行测试，这使得配体发现成为可能，但随着基于廉价的按需制造化合物的化学空间持续增长到数百亿，简单地搜索这个空间成为一个主要挑战。因此，我们开发了ZINC 20，这是ZINC的新版本，具有两个主要的新功能：数十亿个新分子和搜索它们的新方法。作为一个完全枚举的数据库，ZINC可以使用显式的原子级基于图形的方法进行精确搜索，例如SmallWorld用于相似性，Arthor用于模式和子结构搜索，以及3D方法，如对接。通过这些工具和相关工具对新的按需制作复合集进行分析，揭示了惊人的特征。例如，在按需制造的图书馆中，超过97%的核心Bemis-Murcko支架无法从“库存”集合中获得。相应地，新的Bemis-Murcko支架的数量几乎是精心制作的分子的线性部分。因此，与库存组相比，按需制造组中的分子数量增加了88倍，这是基于Bemis-Murcko支架数量增加了16倍。按需制造的文库在结构上也比物理文库更加多样化，圆盘状和球形分子大量增加。新系统可在对接上免费获得。
Identifying and purchasing new small molecules to test in biological assays is enabling for ligand discovery, but as purchasable chemical space continues to grow into the tens of billions based on inexpensive make-on-demand compounds, simply searching this space becomes a major challenge. We have therefore developed ZINC20, a new version of ZINC with two major new features: billions of new molecules and new methods to search them. As a fully enumerated database, ZINC can be searched precisely using explicit atomic-level graph-based methods, such as SmallWorld for similarity, Arthor for pattern and substructure search, as well as 3D methods such as docking. Analysis of the new make-on-demand compound sets by these and related tools reveals startling features. For instance, over 97% of the core Bemis-Murcko scaffolds in make-on-demand libraries are unavailable from “in stock” collections. Correspondingly, the number of new Bemis-Murcko scaffolds is rising almost as a linear fraction of the elaborated molecules. Thus, an 88-fold increase in the number of molecules in the make-on-demand vs the in-stock sets is built upon a 16-fold increase in the number of Bemis-Murcko scaffolds. The make-on-demand library is also more structurally diverse than physical libraries, with a massive increase in disc- and sphere-like shaped molecules. The new system is freely available at zinc20.docking.org.
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影响因子：
5.6
作者：
Irwin JJ;Sterling T;Mysinger MM;Bolstad ES;Coleman RG
通讯作者：
Coleman RG
影响因子：
4.6
作者：
Klingler, Franca-Maria;Gastreich, Marcus;Moroz, Yurii S.
通讯作者：
Moroz, Yurii S.
影响因子：
64.8
作者：
Stein, Reed M.;Kang, Hye Jin;Dubocovich, Margarita L.
通讯作者：
Dubocovich, Margarita L.
DOI：
10.2174/1386207317666140323133841
发表时间：
2014-05-01
影响因子：
1.8
作者：
Arkin, Michelle R.;Ang, Kenny K. H.;Renslo, Adam R.
通讯作者：
Renslo, Adam R.
影响因子：
7.3
作者：
Martin, YC;Kofron, JL;Traphagen, LM
通讯作者：
Traphagen, LM