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In this chapter, we present a variety of case studies where computational methods have been skilfully applied to address questions related to molecular recognition problems. Besides methodological innovations, this chapter aims to illustrate how current relevant chemical biology problems can be studied from a computational chemical biology perspective: dynamics of proteins and structure prediction, protein–protein interactions, complex molecular systems (ribosome, CRISPR/Cas system, Toll-like receptors), nanostructures, and signalling networking. The computational ‘eye’ may help to give some answers to questions regarding the way biological processes take place, and help to raise new questions.

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