图3：DOCKSTRING数据集的聚类分析。(左)使用Tanimoto距离的DBSCAN算法分组的聚类分布。(中)同一簇内分子间(蓝色)和不同簇间(红色)归一化Jaccard距离计数。(右)按支架分组的簇分布。图中信息说明分子的多样性。图4：LCK 与DOCKSTRING数据集中的其他三个靶标对接得分的相关性(以kcal/mol为单位):来自同一家族的靶标...
在这里,作者提出了DOCKSTRING,这是一个用于ML模型的有意义且健壮的分子对接的库。DOCKSTRING由三个组件组成: (1)一个开源Python包直接计算对接分数,(2)一个包含超过260000个分子与蛋白质的对接分数和姿态的数据集,(3)一组药物相关的基准任务。Python包实现了一个鲁棒的配体和蛋白质的前期处理工具,允许非化学专家...
图4:LCK 与DOCKSTRING数据集中的其他三个靶标对接得分的相关性(以kcal/mol为单位):来自同一家族的靶标SRC(左)、核受体ESR2(中)和环氧合酶PTGS2(右)。与靶点独立的分子特性(如logP和QED)不同,根据靶点之间的结构相似性,对接得分显著相关。作者不仅进行了数据集的分析,在文章中还进行了许多的基线测试。展示出...
Edit dockstring Introduced by García-Ortegón et al. in DOCKSTRING: easy molecular docking yields better benchmarks for ligand design Regression dataset for molecular docking scores (predicted molecule-protein binding affinity). Contains ~250,000 molecules against 58 protein targets....
The dockstring dataset was created using: rdkit=2021.03.3 openbabel=3.1.1 python=3.7.10 If you want to reproduce the calculations of the dockstring dataset exactly (or calculate docking scores completely consistent with the dataset) then ideally install these versions of the packages above. ...
Home: https://github.com/dockstring/dockstring Package license: Apache-2.0 Summary: Package for easy ligand preparation and docking with AutoDock Vina against a highly-curated selection of 58 protein targets. One of the three components of the DOCKSTRING bundle (package, dataset, and benchmark ...
arrow_drop_up14 Copy & Edit21 more_vert Docking Simulation Using DockstringNotebookInputOutputLogsComments (11)Output Data An error occurred: Unexpected token '<', "<!doctype "... is not valid JSON Download notebook output navigate_nextminimize content_copyhelp...
It took the Kaggle CPU 116 +/- 26 seconds to dock a molecule using Dockstring. I believe it is unnecessary to dock molecules with shared BBs and the triazine core since they are predictable enough without simulation. If you dock the other 508,983 molecules in the test dataset (22,593 mo...
%{ Multi-line string }.squish # => "Multi-line string" " foo bar \n \t boo".squish # => "foo bar boo"Show source Register or log in to add new notes.Welcome Register Projects Help About Blog APIdock release: IRON STEVE (1.4) If you have any comments, ideas or feedback, ...
v5.0.0.1 - Show latest stable - 0 notes - Class: String 1.0.0 1.1.6 1.2.6 2.0.3 2.1.0 2.2.1 2.3.8 3.0.0 (0) 3.0.9 (-2) 3.1.0 (0) 3.2.1 (0) 3.2.8 (0) 3.2.13 (0) 4.0.2 (3) 4.1.8 (38) 4.2.1 (8) 4.2.7 (0) 4.2.9 (0) 5.0...