Open-Source Machine Learning in Computational Chemistry

被引:14
|
作者
Hagg, Alexander [1 ,2 ]
Kirschner, Karl N. [1 ,3 ]
机构
[1] Univ Appl Sci Bonn Rhein Sieg, Inst Technol Resource & Energy Efficient Engn TREE, D-53757 St Augustin, Germany
[2] Univ Appl Sci Bonn Rhein Sieg, Dept Elect Engn Mech Engn & Tech Journalism, D-53757 St Augustin, Germany
[3] Univ Appl Sci Bonn Rhein Sieg, Dept Comp Sci, D-53757 St Augustin, Germany
关键词
LIGAND BINDING-AFFINITY; CONVOLUTIONAL NEURAL-NETWORK; MOLECULAR-DYNAMICS; ACCURATE PREDICTION; DRUG DISCOVERY; FREE-ENERGY; PROTEIN STRUCTURES; FRAGMENT LINKING; MODELS; SOFTWARE;
D O I
10.1021/acs.jcim.3c00643
中图分类号
R914 [药物化学];
学科分类号
100701 ;
摘要
The field of computational chemistry has seen a significantincreasein the integration of machine learning concepts and algorithms. Inthis Perspective, we surveyed 179 open-source software projects, withcorresponding peer-reviewed papers published within the last 5 years,to better understand the topics within the field being investigatedby machine learning approaches. For each project, we provide a shortdescription, the link to the code, the accompanying license type,and whether the training data and resulting models are made publiclyavailable. Based on those deposited in GitHub repositories, the mostpopular employed Python libraries are identified. We hope that thissurvey will serve as a resource to learn about machine learning orspecific architectures thereof by identifying accessible codes withaccompanying papers on a topic basis. To this end, we also includecomputational chemistry open-source software for generating trainingdata and fundamental Python libraries for machine learning. Basedon our observations and considering the three pillars of collaborativemachine learning work, open data, open source (code), and open models,we provide some suggestions to the community.
引用
收藏
页码:4505 / 4532
页数:28
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