PMID- 22905104
OWN - NLM
STAT- MEDLINE
DCOM- 20130211
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 7
IP  - 8
DP  - 2012
TI  - Predicting HLA class I non-permissive amino acid residues substitutions.
PG  - e41710
LID - 10.1371/journal.pone.0041710 [doi]
LID - e41710
AB  - Prediction of peptide binding to human leukocyte antigen (HLA) molecules is 
      essential to a wide range of clinical entities from vaccine design to stem cell 
      transplant compatibility. Here we present a new structure-based methodology that 
      applies robust computational tools to model peptide-HLA (p-HLA) binding 
      interactions. The method leverages the structural conservation observed in p-HLA 
      complexes to significantly reduce the search space and calculate the system's 
      binding free energy. This approach is benchmarked against existing p-HLA 
      complexes and the prediction performance is measured against a library of 
      experimentally validated peptides. The effect on binding activity across a large 
      set of high-affinity peptides is used to investigate amino acid mismatches 
      reported as high-risk factors in hematopoietic stem cell transplantation.
FAU - Binkowski, T Andrew
AU  - Binkowski TA
AD  - Biosciences Division, Argonne National Laboratory, Midwest Center for Structural 
      Genomics, Argonne, Illinois, United States of America.
FAU - Marino, Susana R
AU  - Marino SR
FAU - Joachimiak, Andrzej
AU  - Joachimiak A
LA  - eng
GR  - U54 GM094585/GM/NIGMS NIH HHS/United States
GR  - GM094585/GM/NIGMS NIH HHS/United States
PT  - Journal Article
PT  - Research Support, N.I.H., Extramural
PT  - Research Support, Non-U.S. Gov't
PT  - Research Support, U.S. Gov't, Non-P.H.S.
DEP - 20120808
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (Amino Acids)
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Peptides)
SB  - IM
MH  - Amino Acid Sequence
MH  - Amino Acid Substitution
MH  - Amino Acids/*chemistry
MH  - Area Under Curve
MH  - Crystallography, X-Ray/methods
MH  - Databases, Protein
MH  - Hematopoietic Stem Cell Transplantation/methods
MH  - Histocompatibility Antigens Class I/*metabolism
MH  - Humans
MH  - Models, Molecular
MH  - Molecular Sequence Data
MH  - Peptides/chemistry
MH  - Protein Binding
MH  - Protein Conformation
MH  - Reproducibility of Results
MH  - Risk
MH  - Risk Factors
MH  - Thermodynamics
PMC - PMC3414483
COIS- Competing Interests: The authors have declared that no competing interests exist.
EDAT- 2012/08/21 06:00
MHDA- 2013/02/12 06:00
PMCR- 2012/08/08
CRDT- 2012/08/21 06:00
PHST- 2012/03/13 00:00 [received]
PHST- 2012/06/27 00:00 [accepted]
PHST- 2012/08/21 06:00 [entrez]
PHST- 2012/08/21 06:00 [pubmed]
PHST- 2013/02/12 06:00 [medline]
PHST- 2012/08/08 00:00 [pmc-release]
AID - PONE-D-12-07503 [pii]
AID - 10.1371/journal.pone.0041710 [doi]
PST - ppublish
SO  - PLoS One. 2012;7(8):e41710. doi: 10.1371/journal.pone.0041710. Epub 2012 Aug 8.