ProteinCCD: Enabling the design of protein truncation constructs for expression and crystallization experiments

Abstract

ProteinCCD (CCD for Crystallographic Construct Design) aims to facilitate a common practice in structural biology, namely the design of several truncation constructs of the protein under investigation, based on experimental data or on sequence analysis tools. ProteinCCD functions as a meta-server, available online at http://xtal.nki.nl/ccd, that collects information from prediction servers concerning secondary structure, disorder, coiled coils, transmembrane segments, domains and domain linkers. It then displays a condensed view of all results against the protein sequence. The user can study the output and choose interactively possible starts and ends for suitable protein constructs. Since the required input to ProteinCCD is the DNA and not the protein sequence, once the starts and ends of constructs are chosen, the software can automatically design the oligonucleotides needed for PCR amplification of all constructs. ProteinCCD outputs a comprehensive view of all constructs and all oligos needed for bookkeeping or for direct copy-paste ordering of the designed oligonucleotides.