my.bionity.com
With an accout for my.bionity.com you can always see everything at a glance – and you can configure your own website and individual newsletter.
by Masahiko Mori, Kei Matsuki, Tomoyuki Maekawa, Mari Tanaka, Busarawan Sriwanthana, Masaru Yokoyama, Koya Ariyoshi
IntroductionClass I HLA's polymorphism has hampered CTL epitope mapping with laborious experiments. Objectives are 1) to evaluate the novel in silico model in predicting previously reported epitopes in comparison with existing program, and 2) to apply the model to predict optimal epitopes with HLA using experimental results.
Materials and MethodsWe have developed a novel in silico epitope prediction method, based on HLA crystal structure and a peptide docking simulation model, calculating the peptide-HLA binding affinity at four amino acid residues in each terminal. It was applied to predict 52 HIV best–defined CTL epitopes from 15-mer overlapping peptides, and its predictive ability was compared with the HLA binding motif-based program of HLArestrictor. It was then used to predict HIV-1 Gag optimal epitopes from previous ELISpot results.
Results43/52 (82.7%) epitopes were detected by the novel model, whereas 37 (71.2%) by HLArestrictor. We also found a significant reduction in epitope detection rates for longer epitopes in HLArestrictor (p = 0.027), but not in the novel model. Improved epitope prediction was also found by introducing both models, especially in specificity (p<0.001). Eight peptides were predicted as novel, immunodominant epitopes in both models.
DiscussionThis novel model can predict optimal CTL epitopes, which were not detected by an existing program. This model is potentially useful not only for narrowing down optimal epitopes, but predicting rare HLA alleles with less information. By introducing different principal models, epitope prediction will be more precise.
| Authors: | Masahiko Mori et al. | |
| Journal: | PLoS ONE | |
| Volume: | 7 | |
| Issue: | 7 | |
| Year: | 2012 | |
| Pages: | e41703 | |
| DOI: | 10.1371/journal.pone.0041703 | |
| Publication date: | 27-07-2012 |
Watchlist
This is where you can add this publication to your personal favourites.
Additional Information
by Jun Zhang, Jianhong Wang, Daoying Geng, Yuxin Li, Donglei Song, Yuxiang Gu Background/Aims The 256-slice CT enables the entire brain to be scanned in a single examination. We evaluated the application of 256-slice whole-brain CT perfusion (CTP) in determining graft patency as well as ... more
by Ikuko Suzuki, Yoshiyuki Tsuboi, Masamichi Shinoda, Kazuo Shibuta, Kuniya Honda, Ayano Katagiri, Masaaki Kiyomoto, Barry J. Sessle, Shingo Matsuura, Kinuyo Ohara, Kentaro Urata, Koichi Iwata To evaluate the involvement of the mitogen-activated protein kinase (MAPK) cascade in o ... more
Increased Rate of Arterial Stiffening with Obesity in Adolescents: A Five-Year Follow-Up Study
by Frida Dangardt, Yun Chen, Krister Berggren, Walter Osika, Peter Friberg Background We prospectively and longitudinally determined the effects of childhood obesity on arterial stiffening and vascular wall changes. Changes in arterial stiffness measured as pulse wave velocity (PWV) and ... more
Genetic variants associated with caffeine intake identified
Two genes in which variation affects intake of caffeine, the most widely consumed stimulant in the world, have been discovered. A team of investigators from the National Cancer Institute, Harvard School of Public Health, Brigham and Women's Hospital, and the University of North Carolina at ... more
Did seasonal flu vaccination increase the risk of infection with pandemic H1N1 flu?
In September 2009, news stories reported that researchers in Canada had found an increased risk of pandemic H1N1 (pH1N1) influenza in people who had previously been vaccinated against seasonal influenza. Their research, consisting of four different studies, has now undergone further scienti ... more
Characterization of grapevine transposons furthers understanding of in vino variety
The grapevine (Vitis vinifera) is a widely cultivated crop that has been subjected to intensive breeding since the Neolithic period (from ~10,500 to ~6,000 years ago). The domestication of grapevine has undergone a selection for traits important for its cultivation and usage. The recent pu ... more
Über CHEMIE.DE
CHEMIE.DE Information Service GmbH runs specialist scientific internet portals. The secret to our success? We are familiar with what we publish.
Advertising at CHEMIE.DE
Our advertising formats support you in getting your message across to a clearly defined target audience.
© 1997-2013 CHEMIE.DE Information Service GmbH, All rights reserved
Netmeeting
