Comparing the Performance of FLUFF-BALL to SEAL-CoMFA with a Large Diverse Estrogen Data Set:  From Relevant Superpositions to Solid Predictions

• Published in: Journal of chemical information and modeling Vol. 45; no. 6; pp. 1874 - 1883
• Main Authors: Korhonen, Samuli-Petrus, Tuppurainen, Kari, Laatikainen, Reino, Peräkylä, Mikael
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 01.11.2005
• Subjects: Algorithms; Animals; Cattle; Estrogens - chemistry; Estrogens - pharmacology; Humans; Knowledge Bases; Ligands; Mice; Models, Statistical; Quantitative Structure-Activity Relationship; Rats; Receptors, Estrogen - drug effects; Receptors, Estrogen - metabolism; Reproducibility of Results; Software; Xenobiotics - chemistry; Xenobiotics - pharmacology
• ISSN: 1549-9596; 1549-960X
• DOI: 10.1021/ci050021i

In this work a template-based molecular mechanistic superposition algorithm FLUFF (Flexible Ligand Unified Force Field) and an accompanying local coordinate QSAR method BALL (Boundless Adaptive Localized Ligand) are validated against the benchmark techniques SEAL (Steric and Electrostatic Alignment) and CoMFA (Comparative Molecular Field Analysis) using a large diverse set of 245 xenoestrogens extracted from the EDKB (Endocrine Disruptor Knowledge Base) maintained by NCTR (National Centre for Toxicological Research). The results indicate that FLUFF is capable of generating relevant superpositions not only for BALL but also for CoMFA, as both techniques give predictive QSAR models. When the BALL and CoMFA methods are compared, it is clear that the BALL algorithm met or even exceeded the results of the standard 3D-QSAR method CoMFA using alignments either from the tailor-made superposition technique FLUFF or the reference method SEAL. The FLUFF-BALL method can be easily automated, and it is computationally light, providing thus a good computational “sieve” capable of fast screening of large molecule libraries.