HLA-Modeler: Automated Homology Modeling of Human Leukocyte Antigens.
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 Å 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.
Science and Technology Systems Division, Computational Science Department, Ryoka Systems Inc., 1-1-2 Oshiage, Sumida-ku, Tokyo 131-0045, Japan.
Shinji
0000-0003-4999-4766
S
Amari
Science and Technology Systems Division, Computational Science Department, Ryoka Systems Inc., 1-1-2 Oshiage, Sumida-ku, Tokyo 131-0045, Japan.
Ryoichi
0000-0002-7598-4740
R
Kataoka
Science and Technology Systems Division, Computational Science Department, Ryoka Systems Inc., 1-1-2 Oshiage, Sumida-ku, Tokyo 131-0045, Japan.
Takashi
T
Ikegami
Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 147 Shimokasuya, Isehara, Kanagawa 259-1143, Japan.
Noriaki
0000-0001-9288-6328
N
Hirayama