A simplified approach to disulfide connectivity prediction from protein sequences

BMC Bioinformatics
Marc VincentPaolo Frasconi

Abstract

Prediction of disulfide bridges from protein sequences is useful for characterizing structural and functional properties of proteins. Several methods based on different machine learning algorithms have been applied to solve this problem and public domain prediction services exist. These methods are however still potentially subject to significant improvements both in terms of prediction accuracy and overall architectural complexity. We introduce new methods for predicting disulfide bridges from protein sequences. The methods take advantage of two new decomposition kernels for measuring the similarity between protein sequences according to the amino acid environments around cysteines. Disulfide connectivity is predicted in two passes. First, a binary classifier is trained to predict whether a given protein chain has at least one intra-chain disulfide bridge. Second, a multiclass classifier (plemented by 1-nearest neighbor) is trained to predict connectivity patterns. The two passes can be easily cascaded to obtain connectivity prediction from sequence alone. We report an extensive experimental comparison on several data sets that have been previously employed in the literature to assess the accuracy of cysteine bonding state and...Continue Reading

References

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Mar 1, 1994·Protein Science : a Publication of the Protein Society·U Hobohm, C Sander
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
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Sep 20, 2005·Proteins·Yu-Ching Chen, Jenn-Kang Hwang
Jul 18, 2006·Nucleic Acids Research·Alessio CeroniPaolo Frasconi
Feb 8, 2007·Proteins·Chih-Hao LuJenn-Kang Hwang
Sep 29, 2009·Nucleic Acids Research·Sven Griep, Uwe Hobohm
Sep 10, 2015·IEEE Transactions on Pattern Analysis and Machine Intelligence·Nikos KomodakisNikos Paragios

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Citations

Feb 11, 2014·BMC Systems Biology·Wei Zhu, Yi-Ping Phoebe Chen
Nov 3, 2015·Evolutionary Bioinformatics Online·Alfonso E Márquez-Chamorro, Jesús S Aguilar-Ruiz
Oct 2, 2014·Current Protocols in Molecular Biology·Na Ke, Mehmet Berkmen
Feb 8, 2021·Computational Biology and Chemistry·Avdesh MishraMd Tamjidul Hoque

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Methods Mentioned

BETA
NMR
X-ray

Software Mentioned

CysPred
SVM light
CSP
DISULFIND
PDBselect
DIpro
DSSP
PSI
SPX
BLAST

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