PMID- 25050981
OWN - NLM
STAT- MEDLINE
DCOM- 20150512
LR  - 20140825
IS  - 1549-960X (Electronic)
IS  - 1549-9596 (Linking)
VI  - 54
IP  - 8
DP  - 2014 Aug 25
TI  - Subangstrom accuracy in pHLA-I modeling by Rosetta FlexPepDock refinement 
      protocol.
PG  - 2233-42
LID - 10.1021/ci500393h [doi]
AB  - Flexible peptides binding to human leukocyte antigen (HLA) play a key role in 
      mediating human immune responses and are also involved in idiosyncratic adverse 
      drug reactions according to recent research. However, the structural 
      determinations of pHLA complexes remain challenging under the present conditions. 
      In this paper, the performance of a new peptide docking method, namely 
      FlexPepDock, was systematically investigated by a benchmark of 30 crystallized 
      structures of peptide-HLA class I complexes. The docking results showed that the 
      near-native pHLA-I models with peptide bb-RMSD less than 2 A were ranked in the 
      top 1 model for 100% (70/70) docking cases, and the subangstrom models with 
      peptide bb-RMSD less than 1 A were ranked in the top 5 lowest-energy models for 
      65.7% (46/70) docking cases. Furthermore, 10 out of 70 docking cases ranked the 
      subangstrom all-atom models in the top 5 lowest-energy models. The results showed 
      that the FlexPepDock can generate high-quality models of pHLA-I complexes and can 
      be widely applied to pHLA-I modeling and mechanism research of peptide-mediated 
      immune responses.
FAU - Liu, Tengfei
AU  - Liu T
AD  - Key Laboratory of Biorheological Science and Technology (Ministry of Education), 
      Chongqing University , Chongqing 400044, China.
FAU - Pan, Xianchao
AU  - Pan X
FAU - Chao, Li
AU  - Chao L
FAU - Tan, Wen
AU  - Tan W
FAU - Qu, Sujun
AU  - Qu S
FAU - Yang, Li
AU  - Yang L
FAU - Wang, Bochu
AU  - Wang B
FAU - Mei, Hu
AU  - Mei H
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140729
PL  - United States
TA  - J Chem Inf Model
JT  - Journal of chemical information and modeling
JID - 101230060
RN  - 0 (Histocompatibility Antigens Class I)
RN  - 0 (Ligands)
RN  - 0 (Peptides)
SB  - IM
MH  - Amino Acid Sequence
MH  - Binding Sites
MH  - Crystallography, X-Ray
MH  - Histocompatibility Antigens Class I/*chemistry/immunology
MH  - Humans
MH  - Ligands
MH  - *Molecular Docking Simulation
MH  - Molecular Sequence Data
MH  - Peptides/*chemistry/immunology
MH  - Protein Binding
MH  - Thermodynamics
EDAT- 2014/07/23 06:00
MHDA- 2015/05/13 06:00
CRDT- 2014/07/23 06:00
PHST- 2014/07/23 06:00 [entrez]
PHST- 2014/07/23 06:00 [pubmed]
PHST- 2015/05/13 06:00 [medline]
AID - 10.1021/ci500393h [doi]
PST - ppublish
SO  - J Chem Inf Model. 2014 Aug 25;54(8):2233-42. doi: 10.1021/ci500393h. Epub 2014 
      Jul 29.