CCD²: design constructs for protein expression, the easy way.

Abstract

Studying the function or structure of proteins usually requires the generation of many protein-truncation constructs for recombinant expression, which is a tedious and error-prone job. CCD² is a software tool designed to facilitate and automate this task. CCD² helps scientists by aggregating the information necessary to design protein-expression constructs. This information includes sequence conservation, secondary structure prediction, domain(s) and disorder detection, post-translational modifications and information on similar (domain) structures that are available in the Protein Data Bank. CCD² then allows users to easily choose the boundaries for protein constructs and automatically generates the primers necessary for construct amplification by polymerase chain reaction. Finally, CCD² provides a quick analysis of the properties of the chosen constructs, together with their DNA vector maps for bookkeeping. The features of CCD² are discussed step by step, showing that it can be a useful tool for laboratories that engage in recombinant protein production for any type of experiment, and in particular for structural biology studies.