Designing string-of-beads vaccines with optimal spacers

Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this,...
Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Schubert, Benjamin [verfasserIn] Kohlbacher, Oliver

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2016

Schlagwörter:	Space Sequence Space Length Human Leucocyte Antigen Epitope Prediction Travel Salesperson Problem

Anmerkung:	© Schubert and Kohlbacher. 2016

Übergeordnetes Werk:	Enthalten in: Genome medicine - London : BioMed Central, 2009, 8(2016), 1 vom: 26. Jan.
Übergeordnetes Werk:	volume:8 ; year:2016 ; number:1 ; day:26 ; month:01

Links:	Volltext

DOI / URN:	10.1186/s13073-016-0263-6

Katalog-ID:	SPR030636051

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allfields	10.1186/s13073-016-0263-6 doi (DE-627)SPR030636051 (SPR)s13073-016-0263-6-e DE-627 ger DE-627 rakwb eng Schubert, Benjamin verfasserin aut Designing string-of-beads vaccines with optimal spacers 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Schubert and Kohlbacher. 2016 Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. Space Sequence (dpeaa)DE-He213 Space Length (dpeaa)DE-He213 Human Leucocyte Antigen (dpeaa)DE-He213 Epitope Prediction (dpeaa)DE-He213 Travel Salesperson Problem (dpeaa)DE-He213 Kohlbacher, Oliver aut Enthalten in Genome medicine London : BioMed Central, 2009 8(2016), 1 vom: 26. Jan. (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:8 year:2016 number:1 day:26 month:01 https://dx.doi.org/10.1186/s13073-016-0263-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2016 1 26 01
spelling	10.1186/s13073-016-0263-6 doi (DE-627)SPR030636051 (SPR)s13073-016-0263-6-e DE-627 ger DE-627 rakwb eng Schubert, Benjamin verfasserin aut Designing string-of-beads vaccines with optimal spacers 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Schubert and Kohlbacher. 2016 Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. Space Sequence (dpeaa)DE-He213 Space Length (dpeaa)DE-He213 Human Leucocyte Antigen (dpeaa)DE-He213 Epitope Prediction (dpeaa)DE-He213 Travel Salesperson Problem (dpeaa)DE-He213 Kohlbacher, Oliver aut Enthalten in Genome medicine London : BioMed Central, 2009 8(2016), 1 vom: 26. Jan. (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:8 year:2016 number:1 day:26 month:01 https://dx.doi.org/10.1186/s13073-016-0263-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2016 1 26 01
allfields_unstemmed	10.1186/s13073-016-0263-6 doi (DE-627)SPR030636051 (SPR)s13073-016-0263-6-e DE-627 ger DE-627 rakwb eng Schubert, Benjamin verfasserin aut Designing string-of-beads vaccines with optimal spacers 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Schubert and Kohlbacher. 2016 Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. Space Sequence (dpeaa)DE-He213 Space Length (dpeaa)DE-He213 Human Leucocyte Antigen (dpeaa)DE-He213 Epitope Prediction (dpeaa)DE-He213 Travel Salesperson Problem (dpeaa)DE-He213 Kohlbacher, Oliver aut Enthalten in Genome medicine London : BioMed Central, 2009 8(2016), 1 vom: 26. Jan. (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:8 year:2016 number:1 day:26 month:01 https://dx.doi.org/10.1186/s13073-016-0263-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2016 1 26 01
allfieldsGer	10.1186/s13073-016-0263-6 doi (DE-627)SPR030636051 (SPR)s13073-016-0263-6-e DE-627 ger DE-627 rakwb eng Schubert, Benjamin verfasserin aut Designing string-of-beads vaccines with optimal spacers 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Schubert and Kohlbacher. 2016 Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. Space Sequence (dpeaa)DE-He213 Space Length (dpeaa)DE-He213 Human Leucocyte Antigen (dpeaa)DE-He213 Epitope Prediction (dpeaa)DE-He213 Travel Salesperson Problem (dpeaa)DE-He213 Kohlbacher, Oliver aut Enthalten in Genome medicine London : BioMed Central, 2009 8(2016), 1 vom: 26. Jan. (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:8 year:2016 number:1 day:26 month:01 https://dx.doi.org/10.1186/s13073-016-0263-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2016 1 26 01
allfieldsSound	10.1186/s13073-016-0263-6 doi (DE-627)SPR030636051 (SPR)s13073-016-0263-6-e DE-627 ger DE-627 rakwb eng Schubert, Benjamin verfasserin aut Designing string-of-beads vaccines with optimal spacers 2016 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Schubert and Kohlbacher. 2016 Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. Space Sequence (dpeaa)DE-He213 Space Length (dpeaa)DE-He213 Human Leucocyte Antigen (dpeaa)DE-He213 Epitope Prediction (dpeaa)DE-He213 Travel Salesperson Problem (dpeaa)DE-He213 Kohlbacher, Oliver aut Enthalten in Genome medicine London : BioMed Central, 2009 8(2016), 1 vom: 26. Jan. (DE-627)594424275 (DE-600)2484394-5 1756-994X nnns volume:8 year:2016 number:1 day:26 month:01 https://dx.doi.org/10.1186/s13073-016-0263-6 kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 8 2016 1 26 01
language	English
source	Enthalten in Genome medicine 8(2016), 1 vom: 26. Jan. volume:8 year:2016 number:1 day:26 month:01
sourceStr	Enthalten in Genome medicine 8(2016), 1 vom: 26. Jan. volume:8 year:2016 number:1 day:26 month:01
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Space Sequence Space Length Human Leucocyte Antigen Epitope Prediction Travel Salesperson Problem
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container_title	Genome medicine
authorswithroles_txt_mv	Schubert, Benjamin @@aut@@ Kohlbacher, Oliver @@aut@@
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author	Schubert, Benjamin
spellingShingle	Schubert, Benjamin misc Space Sequence misc Space Length misc Human Leucocyte Antigen misc Epitope Prediction misc Travel Salesperson Problem Designing string-of-beads vaccines with optimal spacers
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topic_title	Designing string-of-beads vaccines with optimal spacers Space Sequence (dpeaa)DE-He213 Space Length (dpeaa)DE-He213 Human Leucocyte Antigen (dpeaa)DE-He213 Epitope Prediction (dpeaa)DE-He213 Travel Salesperson Problem (dpeaa)DE-He213
topic	misc Space Sequence misc Space Length misc Human Leucocyte Antigen misc Epitope Prediction misc Travel Salesperson Problem
topic_unstemmed	misc Space Sequence misc Space Length misc Human Leucocyte Antigen misc Epitope Prediction misc Travel Salesperson Problem
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format_facet	Elektronische Aufsätze Aufsätze Elektronische Ressource
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title	Designing string-of-beads vaccines with optimal spacers
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title_full	Designing string-of-beads vaccines with optimal spacers
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author_browse	Schubert, Benjamin Kohlbacher, Oliver
container_volume	8
format_se	Elektronische Aufsätze
author-letter	Schubert, Benjamin
doi_str_mv	10.1186/s13073-016-0263-6
title_sort	designing string-of-beads vaccines with optimal spacers
title_auth	Designing string-of-beads vaccines with optimal spacers
abstract	Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. © Schubert and Kohlbacher. 2016
abstractGer	Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. © Schubert and Kohlbacher. 2016
abstract_unstemmed	Abstract String-of-beads polypeptides allow convenient delivery of epitope-based vaccines. The success of a polypeptide relies on efficient processing: constituent epitopes need to be recovered while avoiding neo-epitopes from epitope junctions. Spacers between epitopes are employed to ensure this, but spacer selection is non-trivial. We present a framework to determine optimally the length and sequence of a spacer through multi-objective optimization for human leukocyte antigen class I restricted polypeptides. The method yields string-of-bead vaccines with flexible spacer lengths that increase the predicted epitope recovery rate fivefold while reducing the immunogenicity from neo-epitopes by 44 % compared to designs without spacers. © Schubert and Kohlbacher. 2016
collection_details	GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2009 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2055 GBV_ILN_2111 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700
container_issue	1
title_short	Designing string-of-beads vaccines with optimal spacers
url	https://dx.doi.org/10.1186/s13073-016-0263-6
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author2	Kohlbacher, Oliver
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up_date	2024-07-03T19:15:11.147Z
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