OPM: Orientations of proteins in membranes database

被引:949
作者
Lomize, MA
Lomize, AL [1 ]
Pogozheva, ID
Mosberg, HI
机构
[1] Univ Michigan, Coll Pharm, Ann Arbor, MI 48109 USA
[2] Univ Michigan, Coll Literature Sci & Arts, Ann Arbor, MI 48109 USA
关键词
D O I
10.1093/bioinformatics/btk023
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
The Orientations of Proteins in Membranes (OPM) database provides a collection of transmembrane, monotopic and peripheral proteins from the Protein Data Bank whose spatial arrangements in the lipid bilayer have been calculated theoretically and compared with experimental data. The database allows analysis, sorting and searching of membrane proteins based on their structural classification, species, destination membrane, numbers of transmembrane segments and subunits, numbers of secondary structures and the calculated hydrophobic thickness or tilt angle with respect to the bilayer normal. All coordinate files with the calculated membrane boundaries are available for downloading.
引用
收藏
页码:623 / 625
页数:3
相关论文
共 15 条
[1]   SCOP database in 2004: refinements integrate structure and sequence family data [J].
Andreeva, A ;
Howorth, D ;
Brenner, SE ;
Hubbard, TJP ;
Chothia, C ;
Murzin, AG .
NUCLEIC ACIDS RESEARCH, 2004, 32 :D226-D229
[2]   Insertion of X-ray structures of proteins in membranes [J].
Basyn, F ;
Spies, B ;
Bouffioux, O ;
Thomas, A ;
Brasseur, R .
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2003, 22 (01) :11-21
[3]   The Protein Data Bank [J].
Berman, HM ;
Westbrook, J ;
Feng, Z ;
Gilliland, G ;
Bhat, TN ;
Weissig, H ;
Shindyalov, IN ;
Bourne, PE .
NUCLEIC ACIDS RESEARCH, 2000, 28 (01) :235-242
[4]   The IUBMB-endorsed transporter classification system [J].
Busch, W ;
Saier, MH .
MOLECULAR BIOTECHNOLOGY, 2004, 27 (03) :253-262
[5]   Cys-scanning mutagenesis:: a novel approach to structure-function relationships in polytopic membrane proteins [J].
Frillingos, S ;
Sahin-Tóth, M ;
Wu, JH ;
Kaback, HR .
FASEB JOURNAL, 1998, 12 (13) :1281-1299
[6]   PQS: a protein quaternary structure file server [J].
Henrick, K ;
Thornton, JM .
TRENDS IN BIOCHEMICAL SCIENCES, 1998, 23 (09) :358-361
[7]  
Hubbell WL, 2003, ADV PROTEIN CHEM, V63, P243
[8]   MPtopo: A database of membrane protein topology [J].
Jayasinghe, S ;
Hristova, K ;
White, SH .
PROTEIN SCIENCE, 2001, 10 (02) :455-458
[9]   Lipid-protein interactions in biological membranes: a structural perspective [J].
Lee, AG .
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 2003, 1612 (01) :1-40
[10]   Use of EPR power saturation toanalyze the membrane-docking geometries of peripheral proteins: A applications to C2 domains [J].
Malmberg, NJ ;
Falke, JJ .
ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE, 2005, 34 :71-90