Comparison of MLR, PLS and GA-MLR in QSAR analysis*

Abstract

The use of the internet has evolved in quantitative structure–activity relationship (QSAR) over the past decade with the development of web based activities like the availability of numerous public domain software tools for descriptor calculation and chemometric toolboxes. The importance of chemometrics in QSAR has accelerated in recent years for processing the enormous amount of information in form of predictive mathematical models for large datasets of molecules. With the availability of huge numbers of physicochemical and structural parameters, variable selection became crucial in deriving interpretable and predictive QSAR models. Among several approaches to address this problem, the principle component regression (PCR) and partial least squares (PLS) analyses provide highly predictive QSAR models but being more abstract, they are difficult to understand and interpret. Genetic algorithm (GA) is a stochastic method well suited to the problem of variable selection and to solve optimization problems. Consequently the hybrid approach (GA-MLR) combining GA with multiple linear regression (MLR) may be useful in derivation of highly predictive and interpretable QSAR models. In view of the above, a comparative study of stepwise-MLR, PLS and GA-MLR in deriving QSAR models for datasets of α1-adrenoreceptor antagonists and β3-adrenoreceptor agonists has been carried out using the public domain software Dragon for computing descriptors and free Matlab codes for data modeling.

Keywords:

• Internet resources
• Stepwise MLR
• GA-MLR
• PLS
• β-AR antagonists

Acknowledgements

The authors thank the Director of the CDRI for his interest and gratefully acknowledge the financial grants from DST and CSIR, for the necessary facilities. We also thank Mr A.S. Kushwaha for the technical assistance, one of us (PP) thank the CSIR for the financial assistance in the form of fellowship. CDRI communication no. 6441.

Notes

Presented at CMTPI 2003: Computational Methods in Toxicology and Pharmacology Integrating Internet Resources (Thessaloniki, Greece, September 17–19, 2003).