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J Comput Aided Mol Des. 2012 Jan;26(1):57-67. doi: 10.1007/s10822-011-9530-1. Epub 2011 Dec 21.

Does your model weigh the same as a duck?

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Department of Bioengineering and Therapeutic Sciences, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94158-9001, USA.


Computer-aided drug design is a mature field by some measures, and it has produced notable successes that underpin the study of interactions between small molecules and living systems. However, unlike a truly mature field, fallacies of logic lie at the heart of the arguments in support of major lines of research on methodology and validation thereof. Two particularly pernicious ones are cum hoc ergo propter hoc (with this, therefore because of this) and confirmation bias (seeking evidence that is confirmatory of the hypothesis at hand). These fallacies will be discussed in the context of off-target predictive modeling, QSAR, molecular similarity computations, and docking. Examples will be shown that avoid these problems.

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