Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

被引：224

作者：

Michino, Mayako ^{[1
]}

Abola, Enrique ^{[1
]}

Brooks, Charles L., III ^{[3
,4
]}

Dixon, J. Scott ^{[5
]}

Moult, John ^{[6
]}

Stevens, Raymond C. ^{[1
,2
]}

Olson, Arthur ^{[1
]}

Jurkowski, Wiktor ^{[7
]}

Elofsson, Arne ^{[7
]}

Filipek, Slawomir ^{[8
]}

Pogozheva, Irina ^{[9
]}

Lomize, Andrei ^{[9
]}

Maigret, Bernard ^{[10
]}

Horst, Jeremy ^{[11
]}

Bernard, Brady ^{[11
]}

Iyer, Shyamala ^{[11
]}

Samudrala, Ram ^{[11
]}

Roy, Ambrish ^{[12
]}

Zhang, Yang ^{[12
]}

Sezerman, Osman Ugur ^{[13
]}

Nikiforovich, Gregory V. ^{[14
]}

Taylor, Christina M. ^{[15
]}

Costanzi, Stefano ^{[16
]}

Vorobjev, Y. ^{[17
,18
]}

Bakulina, N. ^{[17
,18
]}

Solovyev, V. ^{[17
,18
]}

Kanou, Kazuhiko ^{[19
,20
]}

Takaya, Daisuke ^{[19
,20
]}

Terashi, Genki ^{[19
,20
]}

Takeda-Shitaka, Mayuko ^{[19
,20
]}

Umeyama, Hideaki ^{[19
,20
]}

Goddard, William A., III ^{[21
]}

Li, Youyong ^{[21
]}

Kim, Soo-Kyung ^{[21
]}

Trzaskowski, Bartosz ^{[21
]}

Abrol, Ravinder ^{[21
]}

Griffith, Adam ^{[21
]}

Katritch, Vsevolod ^{[22
]}

Rueda, Manuel ^{[22
]}

Davis, Ian ^{[23
]}

Barth, Patrick ^{[23
]}

Baker, David ^{[23
]}

Feig, Michael ^{[24
]}

Brylinski, Michal ^{[25
]}

Zhou, Hongyi ^{[25
]}

Lee, Seung Yup ^{[25
]}

Skolnick, Jeffrey ^{[25
]}

Ostopovici-Halip, Liliana ^{[26
]}

Bologa, Cristian ^{[26
]}

Lam, Polo ^{[1
]}

机构：

[1] Scripps Res Inst, Dept Mol Biol, La Jolla, CA 92037 USA

[2] Scripps Res Inst, Dept Chem, La Jolla, CA 92037 USA

[3] Univ Michigan, Dept Chem, Ann Arbor, MI 48109 USA

[4] Univ Michigan, Biophys Program, Ann Arbor, MI 48109 USA

[5] Daylight Chem Informat Syst Inc, Aliso Viejo, CA 92656 USA

[6] Univ Maryland, Inst Biotechnol, Ctr Adv Res Biotechnol, Rockville, MD 20850 USA

[7] Stockholm Univ, Ctr Biomembrane Res, Dept Biochem & Biophys, S-10691 Stockholm, Sweden

[8] Int Inst Mol & Cell Biol, Lab Biomodelling, Warsaw, Poland

[9] Univ Michigan, Peptide Synth & Mol Recognit Lab, Ann Arbor, MI 48109 USA

[10] Nancy Univ, LORIA, Orpailleur Team, Nancy, France

[11] Univ Washington, Computat Biol Grp, Seattle, WA 98195 USA

[12] Univ Kansas, Dept Mol Biosci, Ctr Bioinformat, Lawrence, KS 66045 USA

[13] Sabanci Univ, Biol Sci & Bioengn, Istanbul, Turkey

[14] MolLife Design LLC, St Louis, MO USA

[15] Washington Univ, Dept Biochem & Mol Biophys, St Louis, MO 63130 USA

[16] NIH, Lab Biol Modeling, NIDDKD, Bethesda, MD 20892 USA

[17] Univ London, Royal Holloway, Dept Comp Sci, London TW20 0EX, England

[18] Softberry Inc, Mt Kisco, NY 10549 USA

[19] Kitasato Univ, Sch Pharm, Tokyo 1088641, Japan

[20] RIKEN Syst & Struct Biol Ctr, Yokohama, Kanagawa 2300045, Japan

[21] CALTECH, Mat & Proc Simulat Ctr, Pasadena, CA 91125 USA

[22] Molsoft LLC, San Diego, CA USA

[23] Univ Washington, Dept Biochem, Seattle, WA 98195 USA

[24] Michigan State Univ, Dept Biochem & Mol Biol, E Lansing, MI 48824 USA

[25] Georgia Inst Technol, Ctr Study Syst Biol, Atlanta, GA 30332 USA

[26] Univ New Mexico, Div Biocomp, Albuquerque, NM 87131 USA

[27] Vanderbilt Univ, Ctr Struct Biol, Nashville, TN 37235 USA

[28] Univ N Carolina, Dept Biochem & Biophys, Chapel Hill, NC USA

[29] Complejo Hosp Univ Santiago de Compostela, Fdn Publ Galega Med Xen, Santiago De Compostela, Spain

[30] Univ Helsinki, Fac Pharm, Ctr Drug Res, FIN-00014 Helsinki, Finland

来源：

NATURE REVIEWS DRUG DISCOVERY | 2009年 / 8卷 / 06期

关键词：

PROTEIN-COUPLED RECEPTORS; A(2A) ADENOSINE RECEPTOR; DRUG DISCOVERY; STRUCTURE PREDICTION; CASP7; PREDICTIONS; RHODOPSIN; CRYSTAL; ACCURACY; INSIGHTS; TARGETS;

D O I：

10.1038/nrd2877

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Recent breakthroughs in the determination of the crystal structures of G protein-coupled receptors (GPCRs) have provided new opportunities for structure-based drug design strategies targeting this protein family. With the aim of evaluating the current status of GPCR structure prediction and ligand docking, a community-wide, blind prediction assessment - GPCR Dock 2008 - was conducted in coordination with the publication of the crystal structure of the human adenosine A(2A) receptor bound to the ligand ZM241385. Twenty-nine groups submitted 206 structural models before the release of the experimental structure, which were evaluated for the accuracy of the ligand binding mode and the overall receptor model compared with the crystal structure. This analysis highlights important aspects for success and future development, such as accurate modelling of structurally divergent regions and use of additional biochemical insight such as disulphide bridges in the extracellular loops.

引用

页码：455 / 463

页数：9

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