PyQSAR: A Fast QSAR Modeling Platform Using Machine Learning and Jupyter Notebook

다국어 초록 (Multilingual Abstract)

Understanding the relationship between structure and property is important in current research works. The QSAR/QSPR (Quantitative Structure?Activity Relationship/Quantitative Structure?Property Relationship) is a common method for finding the relationships between the structure and property of compounds. However, traditional methods of performing QSAR analysis rely on multiple software platforms for each step. Here, an integrated standalone python package, PyQSAR, is proposed that combines all QSAR modeling process in one workbench. The efficiency of the package was verified by comparing to 10 previously published works. The results showed high performance of PyQSAR in terms of R 2 with less than half an hour execution time with a typical desktop PC for each test case. The main goal of PyQSAR is the production of reliable QSAR models on a single platform with an easy-to-follow workflow.

참고문헌 (Reference)

1 A. Mayr, 3 : 80-, 2016

2 M. Ester, 96 : 226-, 1996

3 P. Gramatica, 26 : 694-, 2007

4 J. A. Hartigan, 28 : 100-, 1979

5 V. Ruusmann, 6 : 25-, 2014

6 K. Deb, 6 : 182-, 2002

7 K. Deb, 5 : 265-, 1998

8 R. R. Sokal, 1 : 33-, 1962

9 J. J. Bartko, 19 : 3-, 1966

10 B. Bhhatarai, 45 : 1463-, 2011

11 B. Bhhatarai, 23 : 528-, 2010

12 A. Khajeh, 50 : 11337-, 2011

13 Y. Pan, 31 : 41-, 2014

14 P. Gramatica, 18 : 169-, 2007

15 S. v. d. Walt, 13 : 22-, 2011

16 F. Pedregosa, 12 : 2825-, 2011

17 F. Pérez, 9 : 21-, 2007

18 A. Mauri, 56 : 237-, 2006

19 C. W. Yap, 32 : 1466-, 2011

20 I. Guyon, 3 : 1157-, 2003

21 L. L. McQuitty, 20 : 55-, 1960

22 Y.-m. Cheung, 9-15, 2012

23 B. Narasimhan, 54 : 1067-, 2006

24 G. Landrum, "RDKit: Open-Source Cheminformatics"

25 G. Van Rossum, "Python Tutorial"

26 J. Bernard, "Python Data Analysis with Pandas" Springer 37-, 2016

27 R. Todeschini, "Molecular Descriptors for Chemoinformatics:Volume I" John Wiley & Sons 2009

28 L. G. Bang, "Making an interactive QSAR environment in Python/IPython"

29 C. Hill, "Learning Scientific Programming with Python" Cambridge University Press 160-, 2016

30 G. Varoquaux, "Joblib: Running Python function as pipeline jobs"

31 L. S. Aiken, "Handbook of Psychology" Wiley 481-, 2003

32 R. Todeschini, "Handbook of Molecular Descriptors" John Wiley & Sons 2008

33 N. Christianini, "Dictionary of Bioinformatics and Computational Biology" Wiley & Sons 2014

34 "Continuum Analytics"

35 M. Mitchell, "An Introduction to Genetic Algorithms" MIT press 1998