PMID- 20408898
OWN - NLM
STAT- MEDLINE
DCOM- 20100826
LR  - 20220316
IS  - 1365-2567 (Electronic)
IS  - 0019-2805 (Print)
IS  - 0019-2805 (Linking)
VI  - 130
IP  - 3
DP  - 2010 Jul
TI  - MHC class II epitope predictive algorithms.
PG  - 319-28
LID - 10.1111/j.1365-2567.2010.03268.x [doi]
AB  - Major histocompatibility complex class II (MHC-II) molecules sample peptides from 
      the extracellular space, allowing the immune system to detect the presence of 
      foreign microbes from this compartment. To be able to predict the immune response 
      to given pathogens, a number of methods have been developed to predict 
      peptide-MHC binding. However, few methods other than the pioneering 
      TEPITOPE/ProPred method have been developed for MHC-II. Despite recent progress 
      in method development, the predictive performance for MHC-II remains 
      significantly lower than what can be obtained for MHC-I. One reason for this is 
      that the MHC-II molecule is open at both ends allowing binding of peptides 
      extending out of the groove. The binding core of MHC-II-bound peptides is 
      therefore not known a priori and the binding motif is hence not readily 
      discernible. Recent progress has been obtained by including the flanking residues 
      in the predictions. All attempts to make ab initio predictions based on protein 
      structure have failed to reach predictive performances similar to those that can 
      be obtained by data-driven methods. Thousands of different MHC-II alleles exist 
      in humans. Recently developed pan-specific methods have been able to make 
      reasonably accurate predictions for alleles that were not included in the 
      training data. These methods can be used to define supertypes (clusters) of 
      MHC-II alleles where alleles within each supertype have similar binding 
      specificities. Furthermore, the pan-specific methods have been used to make a 
      graphical atlas such as the MHCMotifviewer, which allows for visual comparison of 
      specificities of different alleles.
FAU - Nielsen, Morten
AU  - Nielsen M
AD  - Department of Systems Biology, Technical University of Denmark, Centre for 
      Biological Sequence Analysis, Lyngby, Denmark. mniel@cbs.dtu.dk
FAU - Lund, Ole
AU  - Lund O
FAU - Buus, Soren
AU  - Buus S
FAU - Lundegaard, Claus
AU  - Lundegaard C
LA  - eng
GR  - HHSN26620040006C/PHS HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Review
DEP - 20100412
PL  - England
TA  - Immunology
JT  - Immunology
JID - 0374672
RN  - 0 (Epitopes)
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
MH  - Animals
MH  - Computational Biology/*methods
MH  - Epitopes/chemistry/genetics/*immunology/*metabolism
MH  - Histocompatibility Antigens Class II/chemistry/genetics/*immunology/*metabolism
MH  - Humans
MH  - Protein Binding/immunology
PMC - PMC2913211
EDAT- 2010/04/23 06:00
MHDA- 2010/08/27 06:00
PMCR- 2011/07/01
CRDT- 2010/04/23 06:00
PHST- 2010/04/23 06:00 [entrez]
PHST- 2010/04/23 06:00 [pubmed]
PHST- 2010/08/27 06:00 [medline]
PHST- 2011/07/01 00:00 [pmc-release]
AID - IMM3268 [pii]
AID - 10.1111/j.1365-2567.2010.03268.x [doi]
PST - ppublish
SO  - Immunology. 2010 Jul;130(3):319-28. doi: 10.1111/j.1365-2567.2010.03268.x. Epub 
      2010 Apr 12.