Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

Irina Kufareva; Manuel Rueda; Vsevolod Katritch; Raymond C. Stevens; Ruben Abagyan; Yasushi Yoshikawa; Toshio Furuya; Huisun Lee; Ambrish Roy; John Grime; Joseph Rebehmed; Yang Zhang; Luc Roumen; Iwan J.P. de Esch; Rob Leurs; Chris de Graaf; Youyong Li; Tingjun Hou; Michael M. Mysinger; Dahlia R. Weiss; John J. Irwin; Brian K. Shoichet; Fiona M. McRobb; Ben Capuano; Ian T. Crosby; David K. Chalmers; Elizabeth Yuriev; Qi Wang; Robert H. Mach; David E. Reichert; Gwo Yu Chuang; Didier Rognan; John Simms; Patrick Sexton; Denise Wootten; Dorota Latek; Umesh Ghoshdastider; Slawomir Filipek; LenServer; Andrea Kirkpatrick; Bartosz Trzaskowski; Adam Griffith; Soo Kyung Kim; Ravinder Abrol; William A. Goddard; Nagarajan Vaidehi; Alfonso Lam; Supriyo Bhattacharya; Hubert Li; Gouthaman Balaraman; Michiel Niesen; Sandeep Pal; Victor Solovyev; Yrii Vorobjev; Natalia Bakulina; Thijs Beuming; Stefano Costanzi; Lei Shi; Chris Higgs; Noeris Salam; Dmitry Lupyan; Woody Sherman; Feng Ding; Pradeep Kota; Srinivas Ramachandran; Nikolay V. Dokholyan; Jens Carlsson; Ryan G. Coleman; Hao Fan; Avner Schlessinger; John J. Irwin; Andrej Sali; Brian K. Shoichet; Irina Tikhonova; Irina Pogozheva; Andrei Lomize; Nathan E. Hall; Muhammad Muddassa; Yang Zhang; Ae Nim Pae; Jooyoung Lee; Laura Lopez; Cristian Obiol-Pardo; Jana Selent; Sadia Mahboob; Tim Werner; W. Bret Church; Michal Brylinski; Tadashi Ando; Aysam Guerler; Hongyi Zhou; Jeffrey Skolnick; Henri Xhaard; Wiktor Jurkowski; Arne Elofsson; Ahsan K. Murad; Malgorzata Drwal; Tom B. Dupree; Renate Griffith; Liliana Ostopovici-Halip; Cristian Bologa; K. M. Chen; J. Sun; Patrick Barth; Vladimir Yarov-Yarovoy; David Baker; Bas Vroling; Marijn P.A. Sanders; Sander B. Nabuurs; Gregory V. Nikiforovich

doi:10.1016/j.str.2011.05.012

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

Irina Kufareva, Manuel Rueda, Vsevolod Katritch, Raymond C. Stevens, Ruben Abagyan, Yasushi Yoshikawa, Toshio Furuya, Huisun Lee, Ambrish Roy, John Grime, Joseph Rebehmed, Yang Zhang, Luc Roumen, Iwan J.P. de Esch, Rob Leurs, Chris de Graaf, Youyong Li, Tingjun Hou, Michael M. Mysinger, Dahlia R. WeissJohn J. Irwin, Brian K. Shoichet, Fiona M. McRobb, Ben Capuano, Ian T. Crosby, David K. Chalmers, Elizabeth Yuriev, Qi Wang, Robert H. Mach, David E. Reichert, Gwo Yu Chuang, Didier Rognan, John Simms, Patrick Sexton, Denise Wootten, Dorota Latek, Umesh Ghoshdastider, Slawomir Filipek, LenServer, Andrea Kirkpatrick, Bartosz Trzaskowski, Adam Griffith, Soo Kyung Kim, Ravinder Abrol, William A. Goddard, Nagarajan Vaidehi, Alfonso Lam, Supriyo Bhattacharya, Hubert Li, Gouthaman Balaraman, Michiel Niesen, Sandeep Pal, Victor Solovyev, Yrii Vorobjev, Natalia Bakulina, Thijs Beuming, Stefano Costanzi, Lei Shi, Chris Higgs, Noeris Salam, Dmitry Lupyan, Woody Sherman, Feng Ding, Pradeep Kota, Srinivas Ramachandran, Nikolay V. Dokholyan, Jens Carlsson, Ryan G. Coleman, Hao Fan, Avner Schlessinger, John J. Irwin, Andrej Sali, Brian K. Shoichet, Irina Tikhonova, Irina Pogozheva, Andrei Lomize, Nathan E. Hall, Muhammad Muddassa, Yang Zhang, Ae Nim Pae, Jooyoung Lee, Laura Lopez, Cristian Obiol-Pardo, Jana Selent, Sadia Mahboob, Tim Werner, W. Bret Church, Michal Brylinski, Tadashi Ando, Aysam Guerler, Hongyi Zhou, Jeffrey Skolnick, Henri Xhaard, Wiktor Jurkowski, Arne Elofsson, Ahsan K. Murad, Malgorzata Drwal, Tom B. Dupree, Renate Griffith, Liliana Ostopovici-Halip, Cristian Bologa, K. M. Chen, J. Sun, Patrick Barth, Vladimir Yarov-Yarovoy, David Baker, Bas Vroling, Marijn P.A. Sanders, Sander B. Nabuurs, Gregory V. Nikiforovich

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Abstract

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.

Original language	English (US)
Pages (from-to)	1108-1126
Number of pages	19
Journal	Structure
Volume	19
Issue number	8
DOIs	https://doi.org/10.1016/j.str.2011.05.012
State	Published - Aug 10 2011

All Science Journal Classification (ASJC) codes

Structural Biology
Molecular Biology

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10.1016/j.str.2011.05.012

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Kufareva, I., Rueda, M., Katritch, V., Stevens, R. C., Abagyan, R., Yoshikawa, Y., Furuya, T., Lee, H., Roy, A., Grime, J., Rebehmed, J., Zhang, Y., Roumen, L., de Esch, I. J. P., Leurs, R., de Graaf, C., Li, Y., Hou, T., Mysinger, M. M., ... Nikiforovich, G. V. (2011). Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure, 19(8), 1108-1126. https://doi.org/10.1016/j.str.2011.05.012

@article{47a26885d3e6474595fb2fb7f3212de8,

title = "Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment",

abstract = "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.",

author = "Irina Kufareva and Manuel Rueda and Vsevolod Katritch and Stevens, {Raymond C.} and Ruben Abagyan and Yasushi Yoshikawa and Toshio Furuya and Huisun Lee and Ambrish Roy and John Grime and Joseph Rebehmed and Yang Zhang and Luc Roumen and {de Esch}, {Iwan J.P.} and Rob Leurs and {de Graaf}, Chris and Youyong Li and Tingjun Hou and Mysinger, {Michael M.} and Weiss, {Dahlia R.} and Irwin, {John J.} and Shoichet, {Brian K.} and McRobb, {Fiona M.} and Ben Capuano and Crosby, {Ian T.} and Chalmers, {David K.} and Elizabeth Yuriev and Qi Wang and Mach, {Robert H.} and Reichert, {David E.} and Chuang, {Gwo Yu} and Didier Rognan and John Simms and Patrick Sexton and Denise Wootten and Dorota Latek and Umesh Ghoshdastider and Slawomir Filipek and LenServer and Andrea Kirkpatrick and Bartosz Trzaskowski and Adam Griffith and Kim, {Soo Kyung} and Ravinder Abrol and Goddard, {William A.} and Nagarajan Vaidehi and Alfonso Lam and Supriyo Bhattacharya and Hubert Li and Gouthaman Balaraman and Michiel Niesen and Sandeep Pal and Victor Solovyev and Yrii Vorobjev and Natalia Bakulina and Thijs Beuming and Stefano Costanzi and Lei Shi and Chris Higgs and Noeris Salam and Dmitry Lupyan and Woody Sherman and Feng Ding and Pradeep Kota and Srinivas Ramachandran and Dokholyan, {Nikolay V.} and Jens Carlsson and Coleman, {Ryan G.} and Hao Fan and Avner Schlessinger and Irwin, {John J.} and Andrej Sali and Shoichet, {Brian K.} and Irina Tikhonova and Irina Pogozheva and Andrei Lomize and Hall, {Nathan E.} and Muhammad Muddassa and Yang Zhang and {Nim Pae}, Ae and Jooyoung Lee and Laura Lopez and Cristian Obiol-Pardo and Jana Selent and Sadia Mahboob and Tim Werner and {Bret Church}, W. and Michal Brylinski and Tadashi Ando and Aysam Guerler and Hongyi Zhou and Jeffrey Skolnick and Henri Xhaard and Wiktor Jurkowski and Arne Elofsson and Murad, {Ahsan K.} and Malgorzata Drwal and Dupree, {Tom B.} and Renate Griffith and Liliana Ostopovici-Halip and Cristian Bologa and Chen, {K. M.} and J. Sun and Patrick Barth and Vladimir Yarov-Yarovoy and David Baker and Bas Vroling and Sanders, {Marijn P.A.} and Nabuurs, {Sander B.} and Nikiforovich, {Gregory V.}",

note = "Funding Information: The authors thank Joshua Kunken, Angela Walker, and Katya Kadyshevskaya for their help with data processing, manuscript preparation, and graphic design. The work was supported by NIH Grants R01 GM 071872 and U01 GM094612 to R.A. and U54 GM094618 to R.C.S. ",

year = "2011",

month = aug,

day = "10",

doi = "10.1016/j.str.2011.05.012",

language = "English (US)",

volume = "19",

pages = "1108--1126",

journal = "Structure",

issn = "0969-2126",

publisher = "Cell Press",

number = "8",

}

Kufareva, I, Rueda, M, Katritch, V, Stevens, RC, Abagyan, R, Yoshikawa, Y, Furuya, T, Lee, H, Roy, A, Grime, J, Rebehmed, J, Zhang, Y, Roumen, L, de Esch, IJP, Leurs, R, de Graaf, C, Li, Y, Hou, T, Mysinger, MM, Weiss, DR, Irwin, JJ, Shoichet, BK, McRobb, FM, Capuano, B, Crosby, IT, Chalmers, DK, Yuriev, E, Wang, Q, Mach, RH, Reichert, DE, Chuang, GY, Rognan, D, Simms, J, Sexton, P, Wootten, D, Latek, D, Ghoshdastider, U, Filipek, S, LenServer, Kirkpatrick, A, Trzaskowski, B, Griffith, A, Kim, SK, Abrol, R, Goddard, WA, Vaidehi, N, Lam, A, Bhattacharya, S, Li, H, Balaraman, G, Niesen, M, Pal, S, Solovyev, V, Vorobjev, Y, Bakulina, N, Beuming, T, Costanzi, S, Shi, L, Higgs, C, Salam, N, Lupyan, D, Sherman, W, Ding, F, Kota, P, Ramachandran, S, Dokholyan, NV, Carlsson, J, Coleman, RG, Fan, H, Schlessinger, A, Irwin, JJ, Sali, A, Shoichet, BK, Tikhonova, I, Pogozheva, I, Lomize, A, Hall, NE, Muddassa, M, Zhang, Y, Nim Pae, A, Lee, J, Lopez, L, Obiol-Pardo, C, Selent, J, Mahboob, S, Werner, T, Bret Church, W, Brylinski, M, Ando, T, Guerler, A, Zhou, H, Skolnick, J, Xhaard, H, Jurkowski, W, Elofsson, A, Murad, AK, Drwal, M, Dupree, TB, Griffith, R, Ostopovici-Halip, L, Bologa, C, Chen, KM, Sun, J, Barth, P, Yarov-Yarovoy, V, Baker, D, Vroling, B, Sanders, MPA, Nabuurs, SB & Nikiforovich, GV 2011, 'Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment', Structure, vol. 19, no. 8, pp. 1108-1126. https://doi.org/10.1016/j.str.2011.05.012

TY - JOUR

T1 - Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

AU - Kufareva, Irina

AU - Rueda, Manuel

AU - Katritch, Vsevolod

AU - Stevens, Raymond C.

AU - Abagyan, Ruben

AU - Yoshikawa, Yasushi

AU - Furuya, Toshio

AU - Lee, Huisun

AU - Roy, Ambrish

AU - Grime, John

AU - Rebehmed, Joseph

AU - Zhang, Yang

AU - Roumen, Luc

AU - de Esch, Iwan J.P.

AU - Leurs, Rob

AU - de Graaf, Chris

AU - Li, Youyong

AU - Hou, Tingjun

AU - Mysinger, Michael M.

AU - Weiss, Dahlia R.

AU - Irwin, John J.

AU - Shoichet, Brian K.

AU - McRobb, Fiona M.

AU - Capuano, Ben

AU - Crosby, Ian T.

AU - Chalmers, David K.

AU - Yuriev, Elizabeth

AU - Wang, Qi

AU - Mach, Robert H.

AU - Reichert, David E.

AU - Chuang, Gwo Yu

AU - Rognan, Didier

AU - Simms, John

AU - Sexton, Patrick

AU - Wootten, Denise

AU - Latek, Dorota

AU - Ghoshdastider, Umesh

AU - Filipek, Slawomir

AU - LenServer,

AU - Kirkpatrick, Andrea

AU - Trzaskowski, Bartosz

AU - Griffith, Adam

AU - Kim, Soo Kyung

AU - Abrol, Ravinder

AU - Goddard, William A.

AU - Vaidehi, Nagarajan

AU - Lam, Alfonso

AU - Bhattacharya, Supriyo

AU - Li, Hubert

AU - Balaraman, Gouthaman

AU - Niesen, Michiel

AU - Pal, Sandeep

AU - Solovyev, Victor

AU - Vorobjev, Yrii

AU - Bakulina, Natalia

AU - Beuming, Thijs

AU - Costanzi, Stefano

AU - Shi, Lei

AU - Higgs, Chris

AU - Salam, Noeris

AU - Lupyan, Dmitry

AU - Sherman, Woody

AU - Ding, Feng

AU - Kota, Pradeep

AU - Ramachandran, Srinivas

AU - Dokholyan, Nikolay V.

AU - Carlsson, Jens

AU - Coleman, Ryan G.

AU - Fan, Hao

AU - Schlessinger, Avner

AU - Irwin, John J.

AU - Sali, Andrej

AU - Shoichet, Brian K.

AU - Tikhonova, Irina

AU - Pogozheva, Irina

AU - Lomize, Andrei

AU - Hall, Nathan E.

AU - Muddassa, Muhammad

AU - Zhang, Yang

AU - Nim Pae, Ae

AU - Lee, Jooyoung

AU - Lopez, Laura

AU - Obiol-Pardo, Cristian

AU - Selent, Jana

AU - Mahboob, Sadia

AU - Werner, Tim

AU - Bret Church, W.

AU - Brylinski, Michal

AU - Ando, Tadashi

AU - Guerler, Aysam

AU - Zhou, Hongyi

AU - Skolnick, Jeffrey

AU - Xhaard, Henri

AU - Jurkowski, Wiktor

AU - Elofsson, Arne

AU - Murad, Ahsan K.

AU - Drwal, Malgorzata

AU - Dupree, Tom B.

AU - Griffith, Renate

AU - Ostopovici-Halip, Liliana

AU - Bologa, Cristian

AU - Chen, K. M.

AU - Sun, J.

AU - Barth, Patrick

AU - Yarov-Yarovoy, Vladimir

AU - Baker, David

AU - Vroling, Bas

AU - Sanders, Marijn P.A.

AU - Nabuurs, Sander B.

AU - Nikiforovich, Gregory V.

N1 - Funding Information: The authors thank Joshua Kunken, Angela Walker, and Katya Kadyshevskaya for their help with data processing, manuscript preparation, and graphic design. The work was supported by NIH Grants R01 GM 071872 and U01 GM094612 to R.A. and U54 GM094618 to R.C.S.

PY - 2011/8/10

Y1 - 2011/8/10

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=80051521545&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80051521545&partnerID=8YFLogxK

U2 - 10.1016/j.str.2011.05.012

DO - 10.1016/j.str.2011.05.012

M3 - Article

C2 - 21827947

AN - SCOPUS:80051521545

SN - 0969-2126

VL - 19

SP - 1108

EP - 1126

JO - Structure

JF - Structure

IS - 8

ER -

Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment

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