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Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins

Douglas B Craig and Alan A Dombkowski*

Author Affiliations

Department of Pediatrics, Wayne State University School of Medicine, Detroit, Michigan 48201, USA

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BMC Bioinformatics 2013, 14:346  doi:10.1186/1471-2105-14-346

Published: 1 December 2013

Abstract

Background

Disulfide engineering is an important biotechnological tool that has advanced a wide range of research. The introduction of novel disulfide bonds into proteins has been used extensively to improve protein stability, modify functional characteristics, and to assist in the study of protein dynamics. Successful use of this technology is greatly enhanced by software that can predict pairs of residues that will likely form a disulfide bond if mutated to cysteines.

Results

We had previously developed and distributed software for this purpose: Disulfide by Design (DbD). The original DbD program has been widely used; however, it has a number of limitations including a Windows platform dependency. Here, we introduce Disulfide by Design 2.0 (DbD2), a web-based, platform-independent application that significantly extends functionality, visualization, and analysis capabilities beyond the original program. Among the enhancements to the software is the ability to analyze the B-factor of protein regions involved in predicted disulfide bonds. Importantly, this feature facilitates the identification of potential disulfides that are not only likely to form but are also expected to provide improved thermal stability to the protein.

Conclusions

DbD2 provides platform-independent access and significantly extends the original functionality of DbD. A web server hosting DbD2 is provided at http://cptweb.cpt.wayne.edu/DbD2/ webcite.

Keywords:
Disulfide bond; Protein design; Protein engineering; Bioinformatics