PMID- 21805091
OWN - NLM
STAT- MEDLINE
DCOM- 20120615
LR  - 20211020
IS  - 1573-4919 (Electronic)
IS  - 0300-8177 (Linking)
VI  - 359
IP  - 1-2
DP  - 2012 Jan
TI  - OETMAP: a new feature encoding scheme for MHC class I binding prediction.
PG  - 67-72
LID - 10.1007/s11010-011-1000-5 [doi]
AB  - Deciphering the understanding of T cell epitopes is critical for vaccine 
      development. As recognition of specific peptides bound to Major 
      histocompatibility complex (MHC) class I molecules, cytotoxic T cells are 
      activated. This is the major step to initiate of immune system response. 
      Knowledge of the MHC specificity will enlighten the way of diagnosis, treatment 
      of pathogens as well as peptide vaccine development. So far, a number of methods 
      have been developed to predict MHC/peptide binding. In this article, a novel 
      feature amino acid encoding scheme is proposed to predict MHC/peptide complexes. 
      In the proposed method, we have combined orthonormal encoding (OE) and Taylor's 
      Venn-diagram, and have used Linear support vector machines as the classifier in 
      the tests. We also have compared our method to current feature encoding scheme 
      techniques. The tests have been carried out on comparatively large Human 
      leukocyte antigen (HLA)-A and HLA-B allele peptide three binding datasets 
      extracted from the Immune epitope database and analysis resource. On three 
      datasets experimented, the IC50 cutoff a criteria is used to select the binders 
      and non-binders peptides. Experimental results show that our amino acid encoding 
      scheme leads to better classification performance than other amino acid encoding 
      schemes on a standalone classifier.
FAU - Gok, Murat
AU  - Gok M
AD  - Sakarya University Science Institute, Sakarya, Turkey. muratgok@gmail.com
FAU - Ozcerit, Ahmet Turan
AU  - Ozcerit AT
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110730
PL  - Netherlands
TA  - Mol Cell Biochem
JT  - Molecular and cellular biochemistry
JID - 0364456
RN  - 0 (Epitopes, T-Lymphocyte)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
SB  - IM
MH  - Binding Sites/immunology
MH  - Databases, Protein
MH  - Epitopes, T-Lymphocyte/*immunology
MH  - Histocompatibility Antigens Class I/immunology/*metabolism
MH  - Humans
MH  - Inhibitory Concentration 50
MH  - Methods
MH  - Peptides/immunology/*metabolism
MH  - Support Vector Machine
EDAT- 2011/08/02 06:00
MHDA- 2012/06/16 06:00
CRDT- 2011/08/02 06:00
PHST- 2011/05/06 00:00 [received]
PHST- 2011/07/19 00:00 [accepted]
PHST- 2011/08/02 06:00 [entrez]
PHST- 2011/08/02 06:00 [pubmed]
PHST- 2012/06/16 06:00 [medline]
AID - 10.1007/s11010-011-1000-5 [doi]
PST - ppublish
SO  - Mol Cell Biochem. 2012 Jan;359(1-2):67-72. doi: 10.1007/s11010-011-1000-5. Epub 
      2011 Jul 30.