PRED mafa: A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques

Guang Lan Zhang; David H. O'Connor; Melisa L. Budde; William H. Hildebrand; Jennifer J. Lhost; Vladimir Brusic

doi:10.1145/2147805.2147908

PRED ^mafa: A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques

Guang Lan Zhang, David H. O'Connor, Melisa L. Budde, William H. Hildebrand, Jennifer J. Lhost, Vladimir Brusic

Research output: Chapter in Book/Conference proceeding › Conference contribution › peer-review

1 Citation (Scopus)

Abstract

PREDmafa is a computational system for prediction of peptide binding to three transcriptionally abundant major histocompatibility complex (MHC) class I alleles of Mauritian cynomolgus macaque, an important animal model for the study of human disease. The prediction system utilizes quantitative matrices, which were validated using experimentally determined binders and supported by in vivo studies. We developed 8-mer and 9-mer prediction matrices for Mafa-A1*063:02, 9-mer, 10-mer, and 11-mer prediction matrices for Mafa-B*011:01, and a 9-mer prediction matrix for Mafa-B*075:01. To our knowledge, PRED ^mafa is the first online computational system for predicting peptides that bind Mafa molecules. It is available at http://cvc.dfci.harvard.edu/mafa/.

Original language	English
Title of host publication	2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011
Pages	602-606
Number of pages	5
DOIs	https://doi.org/10.1145/2147805.2147908
Publication status	Published - 2011
Externally published	Yes
Event	2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011 - Chicago, IL, United States Duration: 1 Aug 2011 → 3 Aug 2011

Publication series

Name	2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011

Conference

Conference	2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011
Country/Territory	United States
City	Chicago, IL
Period	1/08/11 → 3/08/11

Keywords

HIV
MHC
Major histocompatibility complex
Mauritian cynomolgus macaques
Online prediction system
SIV
Vaccine design

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1145/2147805.2147908

Cite this

Zhang, G. L., O'Connor, D. H., Budde, M. L., Hildebrand, W. H., Lhost, J. J., & Brusic, V. (2011). PRED ^mafa: A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques. In 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011 (pp. 602-606). (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011). https://doi.org/10.1145/2147805.2147908

Zhang, Guang Lan ; O'Connor, David H. ; Budde, Melisa L. et al. / PRED ^mafa : A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques. 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. pp. 602-606 (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).

@inproceedings{61decd37f426463ba3ef12668ee50a01,

title = "PRED mafa: A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques",

abstract = "PREDmafa is a computational system for prediction of peptide binding to three transcriptionally abundant major histocompatibility complex (MHC) class I alleles of Mauritian cynomolgus macaque, an important animal model for the study of human disease. The prediction system utilizes quantitative matrices, which were validated using experimentally determined binders and supported by in vivo studies. We developed 8-mer and 9-mer prediction matrices for Mafa-A1*063:02, 9-mer, 10-mer, and 11-mer prediction matrices for Mafa-B*011:01, and a 9-mer prediction matrix for Mafa-B*075:01. To our knowledge, PRED mafa is the first online computational system for predicting peptides that bind Mafa molecules. It is available at http://cvc.dfci.harvard.edu/mafa/.",

keywords = "HIV, MHC, Major histocompatibility complex, Mauritian cynomolgus macaques, Online prediction system, SIV, Vaccine design",

author = "Zhang, {Guang Lan} and O'Connor, {David H.} and Budde, {Melisa L.} and Hildebrand, {William H.} and Lhost, {Jennifer J.} and Vladimir Brusic",

note = "Copyright: Copyright 2012 Elsevier B.V., All rights reserved.; 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011 ; Conference date: 01-08-2011 Through 03-08-2011",

year = "2011",

doi = "10.1145/2147805.2147908",

language = "English",

isbn = "9781450307963",

series = "2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011",

pages = "602--606",

booktitle = "2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011",

}

Zhang, GL, O'Connor, DH, Budde, ML, Hildebrand, WH, Lhost, JJ & Brusic, V 2011, PRED ^mafa: A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques. in 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011, pp. 602-606, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, ACM-BCB 2011, Chicago, IL, United States, 1/08/11. https://doi.org/10.1145/2147805.2147908

PRED ^mafa: A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques. / Zhang, Guang Lan; O'Connor, David H.; Budde, Melisa L. et al.
2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. p. 602-606 (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).

Research output: Chapter in Book/Conference proceeding › Conference contribution › peer-review

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AU - Zhang, Guang Lan

AU - O'Connor, David H.

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AU - Hildebrand, William H.

AU - Lhost, Jennifer J.

AU - Brusic, Vladimir

PY - 2011

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AB - PREDmafa is a computational system for prediction of peptide binding to three transcriptionally abundant major histocompatibility complex (MHC) class I alleles of Mauritian cynomolgus macaque, an important animal model for the study of human disease. The prediction system utilizes quantitative matrices, which were validated using experimentally determined binders and supported by in vivo studies. We developed 8-mer and 9-mer prediction matrices for Mafa-A1*063:02, 9-mer, 10-mer, and 11-mer prediction matrices for Mafa-B*011:01, and a 9-mer prediction matrix for Mafa-B*075:01. To our knowledge, PRED mafa is the first online computational system for predicting peptides that bind Mafa molecules. It is available at http://cvc.dfci.harvard.edu/mafa/.

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KW - MHC

KW - Major histocompatibility complex

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KW - Online prediction system

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KW - Vaccine design

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M3 - Conference contribution

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SN - 9781450307963

T3 - 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011

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Zhang GL, O'Connor DH, Budde ML, Hildebrand WH, Lhost JJ, Brusic V. PRED ^mafa: A system for prediction of peptide binding to several MHC class i molecules in cynomolgus macaques. In 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. 2011. p. 602-606. (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011). doi: 10.1145/2147805.2147908