This paper compared different methods to produce fingerprints. Each method was used for virtual screening and their performance was compared. It was concluded that there is not a better method and depending on the problem a particular method can be useful. Also, some metrics for evaluating virtual screening results using fingerprints are mentioned.
Duan, Jianxin, Steven L. Dixon, Jeffrey F. Lowrie, and Woody Sherman. “Analysis and Comparison of 2D Fingerprints: Insights into Database Screening Performance Using Eight Fingerprint Methods.” Journal of Molecular Graphics and Modelling 29, no. 2 (2010): 157–70.
This paper compared different methods to produce fingerprints. Each method was used for virtual screening and their performance was compared. It was concluded that there is not a better method and depending on the problem a particular method can be useful. Also, some metrics for evaluating virtual screening results using fingerprints are mentioned.