PMID- 17090577
OWN - NLM
STAT- MEDLINE
DCOM- 20070306
LR  - 20091104
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Linking)
VI  - 23
IP  - 2
DP  - 2007 Jan 15
TI  - In silico grouping of peptide/HLA class I complexes using structural interaction 
      characteristics.
PG  - 177-83
AB  - MOTIVATION: Classification of human leukocyte antigen (HLA) proteins into 
      supertypes underpins the development of epitope-based vaccines with wide 
      population coverage. Current methods for HLA supertype definition, based on 
      common structural features of HLA proteins and/or their functional binding 
      specificities, leave structural interaction characteristics among different HLA 
      supertypes with antigenic peptides unexplored. METHODS: We describe the use of 
      structural interaction descriptors for the analysis of 68 peptide/HLA class I 
      crystallographic structures. Interaction parameters computed include the number 
      of intermolecular hydrogen bonds between each HLA protein and its corresponding 
      bound peptide, solvent accessibility, gap volume and gap index. RESULTS: The 
      structural interactions patterns of peptide/HLA class I complexes investigated 
      herein vary among individual alleles and may be grouped in a supertype dependent 
      manner. Using the proposed methodology, eight HLA class I supertypes were defined 
      based on existing experimental crystallographic structures which largely overlaps 
      (77% consensus) with the definitions by binding motifs. This mode of 
      classification, which considers conformational information of both peptide and 
      HLA proteins, provides an alternative to the characterization of supertypes using 
      either peptide or HLA protein information alone.
FAU - Tong, Joo Chuan
AU  - Tong JC
AD  - Department of Biochemistry, Yong Loo Lin School of Medicine, National University 
      of Singapore 8 Medical Drive, Singapore 117597.
FAU - Tan, Tin Wee
AU  - Tan TW
FAU - Ranganathan, Shoba
AU  - Ranganathan S
LA  - eng
PT  - Journal Article
DEP - 20061107
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (Histocompatibility Antigens Class I)
SB  - IM
MH  - Alleles
MH  - Artificial Intelligence
MH  - Binding Sites
MH  - Computer Simulation
MH  - Epitope Mapping/*methods
MH  - Histocompatibility Antigens Class I/*chemistry/*classification/immunology
MH  - *Models, Chemical
MH  - Models, Immunological
MH  - Multigene Family/*immunology
MH  - Protein Binding
MH  - Protein Interaction Mapping/*methods
MH  - Sequence Alignment/methods
MH  - Sequence Analysis, Protein/*methods
MH  - Sequence Homology, Amino Acid
MH  - Structure-Activity Relationship
EDAT- 2006/11/09 09:00
MHDA- 2007/03/07 09:00
CRDT- 2006/11/09 09:00
PHST- 2006/11/09 09:00 [pubmed]
PHST- 2007/03/07 09:00 [medline]
PHST- 2006/11/09 09:00 [entrez]
AID - btl563 [pii]
AID - 10.1093/bioinformatics/btl563 [doi]
PST - ppublish
SO  - Bioinformatics. 2007 Jan 15;23(2):177-83. doi: 10.1093/bioinformatics/btl563. 
      Epub 2006 Nov 7.