Community-wide assessment of GPCR structure modelling and ligand docking

GPCR Dock 2008

Mayako Michino, Enrique Abola, Charles L. Brooks, J. Scott Dixon, John Moult, Raymond C. Stevens, Arthur Olson, Wiktor Jurkowski, Arne Elofsson, Slawomir Filipek, Irina Pogozheva, Andrei Lomize, Bernard Maigret, Jeremy Horst, Ambrish Roy, Brady Bernard, Shyamala Iyer, Yang Zhang, Ram Samudrala, Osman Ugur Sezerman & 43 others Gregory V. Nikiforovich, Christina M. Taylor, Stefano Costanzi, Y. Vorobjev, N. Bakulina, V. Solovyev, Kazuhiko Kanou, Daisuke Takaya, Genki Terashi, Mayuko Takeda-Shitaka, Hideaki Umeyama, William A. Goddard, Youyong Li, Soo Kyung Kim, Bartosz Trzaskowski, Ravinder Abrol, Adam Griffith, Vsevolod Katritch, Manuel Rueda, Ruben Abagyan, Ian Davis, Patrick Barth, David Baker, Michael Feig, Michal Brylinski, Hongyi Zhou, Seung Yup Lee, Jeffrey Skolnick, Liliana Ostopovici-Halip, Cristian Bologa, Polo Lam, Ruben Abagyan, Eric S. Dawson, Kristian Kaufmann, Nils Woetzel, Jens Meiler, Feng Ding, Adrian Serohijos, Shuangye Yin, Nikolay Dokholyan, David Rodriguez, Hugo Gutiérrez-de-Teràn, Henri Xhaard

Research output: Contribution to journalArticle

231 Citations (Scopus)

Abstract

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 A2Areceptor 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.

Original languageEnglish (US)
Pages (from-to)455-463
Number of pages9
JournalNature Reviews Drug Discovery
Volume8
Issue number6
DOIs
StatePublished - Jan 1 2009

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G-Protein-Coupled Receptors
Ligands
Drug Design
Structural Models
Protein Transport
Disulfides
Adenosine
Publications

All Science Journal Classification (ASJC) codes

  • Pharmacology
  • Drug Discovery

Cite this

Michino, M., Abola, E., Brooks, C. L., Scott Dixon, J., Moult, J., Stevens, R. C., ... Xhaard, H. (2009). Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews Drug Discovery, 8(6), 455-463. https://doi.org/10.1038/nrd2877
Michino, Mayako ; Abola, Enrique ; Brooks, Charles L. ; Scott Dixon, J. ; Moult, John ; Stevens, Raymond C. ; Olson, Arthur ; Jurkowski, Wiktor ; Elofsson, Arne ; Filipek, Slawomir ; Pogozheva, Irina ; Lomize, Andrei ; Maigret, Bernard ; Horst, Jeremy ; Roy, Ambrish ; Bernard, Brady ; Iyer, Shyamala ; Zhang, Yang ; Samudrala, Ram ; Sezerman, Osman Ugur ; Nikiforovich, Gregory V. ; Taylor, Christina M. ; Costanzi, Stefano ; Vorobjev, Y. ; Bakulina, N. ; Solovyev, V. ; Kanou, Kazuhiko ; Takaya, Daisuke ; Terashi, Genki ; Takeda-Shitaka, Mayuko ; Umeyama, Hideaki ; Goddard, William A. ; Li, Youyong ; Kim, Soo Kyung ; Trzaskowski, Bartosz ; Abrol, Ravinder ; Griffith, Adam ; Katritch, Vsevolod ; Rueda, Manuel ; Abagyan, Ruben ; Davis, Ian ; Barth, Patrick ; Baker, David ; Feig, Michael ; Brylinski, Michal ; Zhou, Hongyi ; Lee, Seung Yup ; Skolnick, Jeffrey ; Ostopovici-Halip, Liliana ; Bologa, Cristian ; Lam, Polo ; Abagyan, Ruben ; Dawson, Eric S. ; Kaufmann, Kristian ; Woetzel, Nils ; Meiler, Jens ; Ding, Feng ; Serohijos, Adrian ; Yin, Shuangye ; Dokholyan, Nikolay ; Rodriguez, David ; Gutiérrez-de-Teràn, Hugo ; Xhaard, Henri. / Community-wide assessment of GPCR structure modelling and ligand docking : GPCR Dock 2008. In: Nature Reviews Drug Discovery. 2009 ; Vol. 8, No. 6. pp. 455-463.
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Michino, M, Abola, E, Brooks, CL, Scott Dixon, J, Moult, J, Stevens, RC, Olson, A, Jurkowski, W, Elofsson, A, Filipek, S, Pogozheva, I, Lomize, A, Maigret, B, Horst, J, Roy, A, Bernard, B, Iyer, S, Zhang, Y, Samudrala, R, Sezerman, OU, Nikiforovich, GV, Taylor, CM, Costanzi, S, Vorobjev, Y, Bakulina, N, Solovyev, V, Kanou, K, Takaya, D, Terashi, G, Takeda-Shitaka, M, Umeyama, H, Goddard, WA, Li, Y, Kim, SK, Trzaskowski, B, Abrol, R, Griffith, A, Katritch, V, Rueda, M, Abagyan, R, Davis, I, Barth, P, Baker, D, Feig, M, Brylinski, M, Zhou, H, Lee, SY, Skolnick, J, Ostopovici-Halip, L, Bologa, C, Lam, P, Abagyan, R, Dawson, ES, Kaufmann, K, Woetzel, N, Meiler, J, Ding, F, Serohijos, A, Yin, S, Dokholyan, N, Rodriguez, D, Gutiérrez-de-Teràn, H & Xhaard, H 2009, 'Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008', Nature Reviews Drug Discovery, vol. 8, no. 6, pp. 455-463. https://doi.org/10.1038/nrd2877

Community-wide assessment of GPCR structure modelling and ligand docking : GPCR Dock 2008. / Michino, Mayako; Abola, Enrique; Brooks, Charles L.; Scott Dixon, J.; Moult, John; Stevens, Raymond C.; Olson, Arthur; Jurkowski, Wiktor; Elofsson, Arne; Filipek, Slawomir; Pogozheva, Irina; Lomize, Andrei; Maigret, Bernard; Horst, Jeremy; Roy, Ambrish; Bernard, Brady; Iyer, Shyamala; Zhang, Yang; Samudrala, Ram; Sezerman, Osman Ugur; Nikiforovich, Gregory V.; Taylor, Christina M.; Costanzi, Stefano; Vorobjev, Y.; Bakulina, N.; Solovyev, V.; Kanou, Kazuhiko; Takaya, Daisuke; Terashi, Genki; Takeda-Shitaka, Mayuko; Umeyama, Hideaki; Goddard, William A.; Li, Youyong; Kim, Soo Kyung; Trzaskowski, Bartosz; Abrol, Ravinder; Griffith, Adam; Katritch, Vsevolod; Rueda, Manuel; Abagyan, Ruben; Davis, Ian; Barth, Patrick; Baker, David; Feig, Michael; Brylinski, Michal; Zhou, Hongyi; Lee, Seung Yup; Skolnick, Jeffrey; Ostopovici-Halip, Liliana; Bologa, Cristian; Lam, Polo; Abagyan, Ruben; Dawson, Eric S.; Kaufmann, Kristian; Woetzel, Nils; Meiler, Jens; Ding, Feng; Serohijos, Adrian; Yin, Shuangye; Dokholyan, Nikolay; Rodriguez, David; Gutiérrez-de-Teràn, Hugo; Xhaard, Henri.

In: Nature Reviews Drug Discovery, Vol. 8, No. 6, 01.01.2009, p. 455-463.

Research output: Contribution to journalArticle

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T2 - GPCR Dock 2008

AU - Michino, Mayako

AU - Abola, Enrique

AU - Brooks, Charles L.

AU - Scott Dixon, J.

AU - Moult, John

AU - Stevens, Raymond C.

AU - Olson, Arthur

AU - Jurkowski, Wiktor

AU - Elofsson, Arne

AU - Filipek, Slawomir

AU - Pogozheva, Irina

AU - Lomize, Andrei

AU - Maigret, Bernard

AU - Horst, Jeremy

AU - Roy, Ambrish

AU - Bernard, Brady

AU - Iyer, Shyamala

AU - Zhang, Yang

AU - Samudrala, Ram

AU - Sezerman, Osman Ugur

AU - Nikiforovich, Gregory V.

AU - Taylor, Christina M.

AU - Costanzi, Stefano

AU - Vorobjev, Y.

AU - Bakulina, N.

AU - Solovyev, V.

AU - Kanou, Kazuhiko

AU - Takaya, Daisuke

AU - Terashi, Genki

AU - Takeda-Shitaka, Mayuko

AU - Umeyama, Hideaki

AU - Goddard, William A.

AU - Li, Youyong

AU - Kim, Soo Kyung

AU - Trzaskowski, Bartosz

AU - Abrol, Ravinder

AU - Griffith, Adam

AU - Katritch, Vsevolod

AU - Rueda, Manuel

AU - Abagyan, Ruben

AU - Davis, Ian

AU - Barth, Patrick

AU - Baker, David

AU - Feig, Michael

AU - Brylinski, Michal

AU - Zhou, Hongyi

AU - Lee, Seung Yup

AU - Skolnick, Jeffrey

AU - Ostopovici-Halip, Liliana

AU - Bologa, Cristian

AU - Lam, Polo

AU - Abagyan, Ruben

AU - Dawson, Eric S.

AU - Kaufmann, Kristian

AU - Woetzel, Nils

AU - Meiler, Jens

AU - Ding, Feng

AU - Serohijos, Adrian

AU - Yin, Shuangye

AU - Dokholyan, Nikolay

AU - Rodriguez, David

AU - Gutiérrez-de-Teràn, Hugo

AU - Xhaard, Henri

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Y1 - 2009/1/1

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Michino M, Abola E, Brooks CL, Scott Dixon J, Moult J, Stevens RC et al. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews Drug Discovery. 2009 Jan 1;8(6):455-463. https://doi.org/10.1038/nrd2877