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Nucleic Acids Research Advance Access originally published online on April 24, 2009
Nucleic Acids Research 2009 37(Web Server issue):W402-W405; doi:10.1093/nar/gkp256
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W402-W405
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Wijnand T. M. Mooij1, Eirini Mitsiki1 and Anastassis Perrakis1,*

1Department of Biochemistry, NKI, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands

*To whom correspondence should be addressed. Tel: +31205121951; Fax: +31205121954; Email: a.perrakis{at}nki.nl

Received December 15, 2008. Revised April 2, 2009. Accepted April 6, 2009.

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.


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