Status of GPCR Modeling and Docking as Reflected by Community-wide GPCR Dock 2010 Assessment

被引：223

作者：

Kufareva, Irina ^{[2
]}

Rueda, Manuel ^{[2
]}

Katritch, Vsevolod ^{[2
,3
]}

Stevens, Raymond C. ^{[1
]}

Abagyan, Ruben ^{[2
,3
]}

Yoshikawa, Yasushi ^{[4
]}

Furuya, Toshio ^{[4
]}

Lee, Huisun ^{[5
]}

Roy, Ambrish ^{[5
]}

Grime, John ^{[5
]}

Rebehmed, Joseph ^{[5
]}

Zhang, Yang ^{[5
,30
]}

Roumen, Luc ^{[6
]}

de Esch, Iwan J. P. ^{[6
]}

Leurs, Rob ^{[6
]}

de Graaf, Chris ^{[6
]}

Li, Youyong ^{[7
,8
]}

Hou, Tingjun ^{[7
,8
]}

Mysinger, Michael M. ^{[9
]}

Weiss, Dahlia R. ^{[9
]}

Irwin, John J. ^{[9
,25
]}

Shoichet, Brian K. ^{[9
,25
]}

McRobb, Fiona M. ^{[10
]}

Capuano, Ben ^{[10
]}

Crosby, Ian T. ^{[10
]}

Chalmers, David K. ^{[10
]}

Yuriev, Elizabeth ^{[10
]}

Wang, Qi ^{[11
]}

Mach, Robert H. ^{[11
]}

Reichert, David E. ^{[11
]}

Chuang, Gwo-Yu ^{[12
]}

Rognan, Didier ^{[12
]}

Simms, John ^{[13
]}

Sexton, Patrick ^{[13
]}

Wootten, Denise ^{[13
]}

Latek, Dorota ^{[14
]}

Ghoshdastider, Umesh ^{[14
]}

Filipek, Slawomir ^{[14
]}

Kirkpatrick, Andrea ^{[16
]}

Trzaskowski, Bartosz ^{[16
]}

Griffith, Adam ^{[16
]}

Kim, Soo-Kyung ^{[16
]}

Abrol, Ravinder ^{[16
]}

Goddard, William A., III ^{[16
]}

Vaidehi, Nagarajan ^{[17
]}

Lam, Alfonso ^{[17
]}

Bhattacharya, Supriyo ^{[17
]}

Li, Hubert ^{[17
]}

Balaraman, Gouthaman ^{[17
]}

Niesen, Michiel ^{[17
]}

机构：

[1] Scripps Res Inst, Dept Mol Biol, 10666 N Torrey Pines Rd, La Jolla, CA 92037 USA

[2] Univ Calif San Diego, Skaggs Sch Pharm & Pharmaceut Sci, La Jolla, CA 92039 USA

[3] San Diego Supercomp Ctr, La Jolla, CA 92039 USA

[4] PharmaDesign Inc, Res & Dev Div, Tokyo, Japan

[5] Univ Michigan, Ctr Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[6] Vrije Univ Amsterdam, Dept Med Chem, Amsterdam, Netherlands

[7] Soochow Univ, Inst Funct Nano Soft Mat FUNSOM, Suzhou, Peoples R China

[8] Soochow Univ, Jiangsu Key Lab Carbon Based Funct Mat Devices, Suzhou, Peoples R China

[9] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA USA

[10] Monash Univ, Monash Inst Pharmaceut Sci, Med Chem & Drug Act, Melbourne, Vic, Australia

[11] Washington Univ, Mallinckrodt Inst Radiol, Div Radiol Sci, St Louis, MO USA

[12] Univ Strasbourg, Struct Chemogen, Illkirch Graffenstaden, France

[13] Monash Univ, Pharmacol, Melbourne, Vic, Australia

[14] Univ Warsaw, Fac Chem, Warsaw, Poland

[15] Soochow Univ, Sch Comp Sci & Technol, Suzhou, Peoples R China

[16] CALTECH, Chem, Pasadena, CA 91125 USA

[17] City Hope Natl Med Ctr, Beckman Res Inst, Div Immunol, Duarte, CA USA

[18] Evotec Ltd, Computat Chem & Mol Modeling, Abingdon, Oxon, England

[19] Univ London, Dept Comp Sci, Royal Holloway, Egham, Surrey, England

[20] Softberry Inc, Mt Kisco, NY USA

[21] Schrodinger Inc, Lab Biol Modeling, New York, NY USA

[22] Natl Inst Diabet & Digest & Kidney Dis, NIH, Bethesda, MD USA

[23] Cornell Univ, Weill Cornell Med Coll, New York, NY 10021 USA

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

[25] Univ Calif San Francisco, Dept Pharmaceut Chem, San Francisco, CA USA

[26] Queens Univ, Sch Pharm, Ctr Med Biol, Belfast, Antrim, North Ireland

[27] Univ Michigan, Coll Pharm, Dept Med Chem, Ann Arbor, MI 48109 USA

[28] Monash Univ, Monash Inst Pharmaceut Sci, Drug Discovery Biol, Parkville, Vic, Australia

[29] Korea Inst Adv Study, Sch Computat Sci, Seoul, South Korea

[30] Univ Michigan, Ctr Computat Med & Bioinformat, Ann Arbor, MI 48109 USA

[31] Korea Inst Sci & Technol, Ctr Neuromed, Seoul, South Korea

[32] Pompeu Fabra Univ, Comp Assisted Drug Design, Barcelona, Spain

[33] Univ Sydney, Biomol Struct & Informat, Fac Pharm, Sydney, NSW, Australia

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

[35] Univ Helsinki, Ctr Drug Res, Fac Pharm, Helsinki, Finland

[36] Stockholm Univ, Ctr Biomembrane Res, Stockholm, Sweden

[37] Univ New S Wales, Sch Med Sci, Sydney, NSW, Australia

[38] Romanian Acad, Inst Chem, Timisoara, Romania

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

[40] Baylor Coll Med, Verna & Marrs McLean Dept Biochem & Mol Biol, Houston, TX 77030 USA

[41] Baylor Coll Med, Dept Pharmacol, Houston, TX 77030 USA

[42] Univ Washington, Pharmacol, Seattle, WA 98195 USA

[43] Radboud Univ Nijmegen, Computat Drug Discovery Grp, Ctr Mol & Biomol Informat, Med Ctr, Nijmegen, Netherlands

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

来源：

STRUCTURE | 2011年 / 19卷 / 08期

关键词：

PROTEIN-COUPLED RECEPTORS; CRYSTAL-STRUCTURE; LIGAND DOCKING; STRUCTURE PREDICTION; SMALL-MOLECULE; FLEXIBILITY; COMPLEX; IDENTIFICATION; AGONISTS; PROGRESS;

D O I：

10.1016/j.str.2011.05.012

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The community-wide GPCR Dock assessment is conducted to evaluate the status of molecular modeling and ligand docking for human G protein-coupled receptors. The present round of the assessment was based on the recent structures of dopamine D3 and CXCR4 chemokine receptors bound to small molecule antagonists and CXCR4 with a synthetic cyclopeptide. Thirty-five groups submitted their receptor-ligand complex structure predictions prior to the release of the crystallographic coordinates. With closely related homology modeling templates, as for dopamine D3 receptor, and with incorporation of biochemical and QSAR data, modern computational techniques predicted complex details with accuracy approaching experimental. In contrast, CXCR4 complexes that had less-characterized interactions and only distant homology to the known GPCR structures still remained very challenging. The assessment results provide guidance for modeling and crystallographic communities in method development and target selection for further expansion of the structural coverage of the GPCR universe.

引用

页码：1108 / 1126

页数：19

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