PMID- 25374692
OWN - NLM
STAT- PubMed-not-MEDLINE
DCOM- 20141106
LR  - 20211021
IS  - 2090-2069 (Print)
IS  - 2090-2077 (Electronic)
IS  - 2090-2077 (Linking)
VI  - 2013
DP  - 2013
TI  - HLA-Modeler: Automated Homology Modeling of Human Leukocyte Antigens.
PG  - 690513
LID - 10.1155/2013/690513 [doi]
LID - 690513
AB  - The three-dimensional (3D) structures of human leukocyte antigen (HLA) molecules 
      are indispensable for the studies on the functions at molecular level. We have 
      developed a homology modeling system named HLA-modeler specialized in the HLA 
      molecules. Segment matching algorithm is employed for modeling and the 
      optimization of the model is carried out by use of the PFROSST force field 
      considering the implicit solvent model. In order to efficiently construct the 
      homology models, HLA-modeler uses a local database of the 3D structures of HLA 
      molecules. The structure of the antigenic peptide-binding site is important for 
      the function and the 3D structure is highly conserved between various alleles. 
      HLA-modeler optimizes the use of this structural motif. The leave-one-out 
      cross-validation using the crystal structures of class I and class II HLA 
      molecules has demonstrated that the rmsds of nonhydrogen atoms of the sites 
      between homology models and crystal structures are less than 1.0 A in most cases. 
      The results have indicated that the 3D structures of the antigenic 
      peptide-binding sites can be reproduced by HLA-modeler at the level almost 
      corresponding to the crystal structures.
FAU - Amari, Shinji
AU  - Amari S
AUID- ORCID: 0000-0003-4999-4766
AD  - Science and Technology Systems Division, Computational Science Department, Ryoka 
      Systems Inc., 1-1-2 Oshiage, Sumida-ku, Tokyo 131-0045, Japan.
FAU - Kataoka, Ryoichi
AU  - Kataoka R
AUID- ORCID: 0000-0002-7598-4740
AD  - Science and Technology Systems Division, Computational Science Department, Ryoka 
      Systems Inc., 1-1-2 Oshiage, Sumida-ku, Tokyo 131-0045, Japan.
FAU - Ikegami, Takashi
AU  - Ikegami T
AD  - Science and Technology Systems Division, Computational Science Department, Ryoka 
      Systems Inc., 1-1-2 Oshiage, Sumida-ku, Tokyo 131-0045, Japan.
FAU - Hirayama, Noriaki
AU  - Hirayama N
AUID- ORCID: 0000-0001-9288-6328
AD  - Basic Medical Science and Molecular Medicine, Tokai University School of 
      Medicine, 147 Shimokasuya, Isehara, Kanagawa 259-1143, Japan.
LA  - eng
PT  - Journal Article
DEP - 20131127
PL  - United States
TA  - Int J Med Chem
JT  - International journal of medicinal chemistry
JID - 101622092
PMC - PMC4207409
EDAT- 2013/01/01 00:00
MHDA- 2013/01/01 00:01
PMCR- 2013/11/27
CRDT- 2014/11/07 06:00
PHST- 2013/08/10 00:00 [received]
PHST- 2013/10/08 00:00 [revised]
PHST- 2013/10/08 00:00 [accepted]
PHST- 2014/11/07 06:00 [entrez]
PHST- 2013/01/01 00:00 [pubmed]
PHST- 2013/01/01 00:01 [medline]
PHST- 2013/11/27 00:00 [pmc-release]
AID - 10.1155/2013/690513 [doi]
PST - ppublish
SO  - Int J Med Chem. 2013;2013:690513. doi: 10.1155/2013/690513. Epub 2013 Nov 27.