A review of algorithmic techniques for disulfide-bond determination

Abstract

Disulfide bonds play an important role in understanding protein folding, evolution, and in studies related to determining structural and functional properties of specific proteins. At the state-of-the-art, a large number of computational techniques have been proposed for determining disulfide bonds. Operating across the gamut of input data, from pure sequence-based information to spectra from mass spectrometry, these techniques provide researchers with a variety of methodological choices and trade-offs. Techniques for disulfide-bond determination are also underpinned by a rich variety of algorithmic formulations. Analysis of these algorithms can provide valuable cues towards choosing a particular technique and understanding its results. Further, their study is critical in developing the next generation of techniques. This paper discusses the importance and applicability of disulfide-bond determination in understanding protein structure and function and provides a detailed review of computational approaches to this problem.

Bacterial thiol oxidoreductases — from basic research to new antibacterial strategies

“…Also, in silico structural modeling supplies informative data about the presence of consecutive or nonconsecutive disulfides. Recently, several algorithmic techniques have been elaborated to determine the presence of disulfides in a protein of interest (Becker et al 2013; Lin and Tseng 2010; Marquez-Chamorro and Aguilar-Ruiz 2015; Singh 2008). …”

<formula formulatype="inline"><tex Notation="TeX">${\rm MS2DB}+$</tex></formula>: A Software for Determination of Disulfide Bonds Using Multi-Ion Analysis

“…Methods for determining S-S bonds can be broadly grouped into two categories: those that use sequence-level information to predict S-S bonds, and those based on data from mass spectrometry (MS), crystallography or NMR. For a detailed review of these methods, we refer the reader to [1] and references therein. Of the above, MS-based approaches are especially interesting due to their high accuracy.…”

The MS2DB<formula formulatype="inline"><tex Notation="TeX">${++}$</tex> </formula> Webserver: Disulfide Bond Determination Through Evidence Combination

“…A T THE CURRENT state of the art, multiple classes of computational methods exist for determining disulfide (S-S) bonds [1]. Yet no single class of methods is known to perform accurately across a diverse set of molecules.…”