Standard
Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment : meeting new challenges. / Kufareva, Irina; Katritch, Vsevolod; Biggin, Phil; Kim, Minsup; Park, Kichul; Jung, Sang Won; Cho, Art E.; Sands, Zara A.; Ostopovici-Halip, Liliana; Bologa, Cristian G.; Norn, Christoffer; Brylinski, Michal; Skolnick, Jeffrey; Keränen, Henrik; Lenselink, Bart E.; Van Westen, Gerard; Overington, John P.; De Teráán, Hugo Gutiérrez; Isberg, Vignir; Fidom, Kimberley M.; Lehto, Thomas M.; Gloriam, David E.; Ghosh, Anirban; Sonavane, Uddhavesh; Joshi, Rajendra; Xia, Jie; Hsieh, Jui Hua; Zhang, Liangren; Wang, Xiang Simon; Vogel, Horst; Yuan, Shuguang; Feng, X.; Chen, M.; Ambia, J.; Barth, P.; Gageat, Cédric; Stepniewski, Michal; Xhaard, Henri; Kelm, Sebastian; Pitt, William R.; Shi, Jiye; Larsen, Adrien; Li, Hubert; Wagner, Jeffrey; Bhattacharya, Supriyo; Vaidehi, Nagarajan; Kanou, Kazuhiko; Cvicek, Vaclav; Kim, Soo Kyung; Trzaskowski, Bartosz; Goddard, William A.; Abrol, Ravinder; Selvam, Balaji; Tikhonova, Irina G.; Cuzzolin, Alberto; Sabbadin, Davide; Ciancetta, Antonella; Moro, Stefano; Freyd, Thibaud; Gabrielsen, Mari; Kristiansen, Kurt; Sylte, Ingebrigt; Gaffney, Kevin J.; Petasis, Nicos A.; Latek, Dorota; Bajda, Marek; Młynarczyk, Krzysztof; Filipek, Sławomir; López, Laura; Kuiper, Michael; Beuming, Thijs; Perez-Aguilar, Jose Manuel; Wang, Ray Yu Ruei; Park, Hahnbeom; Greisen, Per; Song, Yifan; DiMaio, Frank; Baker, David; Shin, Woong Hee; Heo, Lim; Lee, Gyu Rie; Seok, Chaok; Yang, Jianyi; Zhang, Yang; Ponassi, Marco; Rosano, Camillo; Cheremovskiy, Georgy; Grudinin, Sergei; Chaudhari, Rajan; Heim, Andrew J.; Li, Zhijun; Lv, Qiang; Grigorov, Martin G.; Hu, Xin; Sun, Hongmao; Shen, Min; Southall, Noel; Jadhav, Ajit; Rodríguez, David; Ranganathan, Anirudh; Carlsson, Jens; Najmanovich, Rafael; Durdagi, Serdar; De March, Claire; Diharce, Julien; Golebiowski, Jérôme; Antonczak, Serge; Fiorucci, Sébastien; Nguyen, Elizabeth; Meiler, Jens; Gutcaits, Aleksandrs; Marti-Solano, Maria; Pastor, Manuel; Selent, Jana; Stevens, Raymond C.; Abagyan, Ruben.
In:
Structure, Vol. 22, No. 8, 2014, p. 1120-1139.
Research output: Contribution to journal › Journal article › Research › peer-review
Harvard
Kufareva, I, Katritch, V, Biggin, P, Kim, M, Park, K, Jung, SW, Cho, AE, Sands, ZA, Ostopovici-Halip, L, Bologa, CG, Norn, C, Brylinski, M, Skolnick, J, Keränen, H, Lenselink, BE, Van Westen, G, Overington, JP, De Teráán, HG, Isberg, V, Fidom, KM, Lehto, TM
, Gloriam, DE, Ghosh, A, Sonavane, U, Joshi, R, Xia, J, Hsieh, JH, Zhang, L, Wang, XS, Vogel, H, Yuan, S, Feng, X, Chen, M, Ambia, J, Barth, P, Gageat, C, Stepniewski, M, Xhaard, H, Kelm, S, Pitt, WR, Shi, J, Larsen, A, Li, H, Wagner, J, Bhattacharya, S, Vaidehi, N, Kanou, K, Cvicek, V, Kim, SK, Trzaskowski, B, Goddard, WA, Abrol, R, Selvam, B, Tikhonova, IG, Cuzzolin, A, Sabbadin, D, Ciancetta, A, Moro, S, Freyd, T, Gabrielsen, M, Kristiansen, K, Sylte, I, Gaffney, KJ, Petasis, NA, Latek, D, Bajda, M, Młynarczyk, K, Filipek, S, López, L, Kuiper, M, Beuming, T, Perez-Aguilar, JM, Wang, RYR, Park, H, Greisen, P, Song, Y, DiMaio, F, Baker, D, Shin, WH, Heo, L, Lee, GR, Seok, C, Yang, J, Zhang, Y, Ponassi, M, Rosano, C, Cheremovskiy, G, Grudinin, S, Chaudhari, R, Heim, AJ, Li, Z, Lv, Q, Grigorov, MG, Hu, X, Sun, H, Shen, M, Southall, N, Jadhav, A, Rodríguez, D, Ranganathan, A, Carlsson, J, Najmanovich, R, Durdagi, S, De March, C, Diharce, J, Golebiowski, J, Antonczak, S, Fiorucci, S, Nguyen, E, Meiler, J, Gutcaits, A, Marti-Solano, M, Pastor, M, Selent, J, Stevens, RC & Abagyan, R 2014, '
Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges',
Structure, vol. 22, no. 8, pp. 1120-1139.
https://doi.org/10.1016/j.str.2014.06.012APA
Kufareva, I., Katritch, V., Biggin, P., Kim, M., Park, K., Jung, S. W., Cho, A. E., Sands, Z. A., Ostopovici-Halip, L., Bologa, C. G., Norn, C., Brylinski, M., Skolnick, J., Keränen, H., Lenselink, B. E., Van Westen, G., Overington, J. P., De Teráán, H. G., Isberg, V., ... Abagyan, R. (2014).
Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.
Structure,
22(8), 1120-1139.
https://doi.org/10.1016/j.str.2014.06.012Vancouver
Kufareva I, Katritch V, Biggin P, Kim M, Park K, Jung SW et al.
Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges.
Structure. 2014;22(8):1120-1139.
https://doi.org/10.1016/j.str.2014.06.012Author
Kufareva, Irina ; Katritch, Vsevolod ; Biggin, Phil ; Kim, Minsup ; Park, Kichul ; Jung, Sang Won ; Cho, Art E. ; Sands, Zara A. ; Ostopovici-Halip, Liliana ; Bologa, Cristian G. ; Norn, Christoffer ; Brylinski, Michal ; Skolnick, Jeffrey ; Keränen, Henrik ; Lenselink, Bart E. ; Van Westen, Gerard ; Overington, John P. ; De Teráán, Hugo Gutiérrez ; Isberg, Vignir ; Fidom, Kimberley M. ; Lehto, Thomas M. ; Gloriam, David E. ; Ghosh, Anirban ; Sonavane, Uddhavesh ; Joshi, Rajendra ; Xia, Jie ; Hsieh, Jui Hua ; Zhang, Liangren ; Wang, Xiang Simon ; Vogel, Horst ; Yuan, Shuguang ; Feng, X. ; Chen, M. ; Ambia, J. ; Barth, P. ; Gageat, Cédric ; Stepniewski, Michal ; Xhaard, Henri ; Kelm, Sebastian ; Pitt, William R. ; Shi, Jiye ; Larsen, Adrien ; Li, Hubert ; Wagner, Jeffrey ; Bhattacharya, Supriyo ; Vaidehi, Nagarajan ; Kanou, Kazuhiko ; Cvicek, Vaclav ; Kim, Soo Kyung ; Trzaskowski, Bartosz ; Goddard, William A. ; Abrol, Ravinder ; Selvam, Balaji ; Tikhonova, Irina G. ; Cuzzolin, Alberto ; Sabbadin, Davide ; Ciancetta, Antonella ; Moro, Stefano ; Freyd, Thibaud ; Gabrielsen, Mari ; Kristiansen, Kurt ; Sylte, Ingebrigt ; Gaffney, Kevin J. ; Petasis, Nicos A. ; Latek, Dorota ; Bajda, Marek ; Młynarczyk, Krzysztof ; Filipek, Sławomir ; López, Laura ; Kuiper, Michael ; Beuming, Thijs ; Perez-Aguilar, Jose Manuel ; Wang, Ray Yu Ruei ; Park, Hahnbeom ; Greisen, Per ; Song, Yifan ; DiMaio, Frank ; Baker, David ; Shin, Woong Hee ; Heo, Lim ; Lee, Gyu Rie ; Seok, Chaok ; Yang, Jianyi ; Zhang, Yang ; Ponassi, Marco ; Rosano, Camillo ; Cheremovskiy, Georgy ; Grudinin, Sergei ; Chaudhari, Rajan ; Heim, Andrew J. ; Li, Zhijun ; Lv, Qiang ; Grigorov, Martin G. ; Hu, Xin ; Sun, Hongmao ; Shen, Min ; Southall, Noel ; Jadhav, Ajit ; Rodríguez, David ; Ranganathan, Anirudh ; Carlsson, Jens ; Najmanovich, Rafael ; Durdagi, Serdar ; De March, Claire ; Diharce, Julien ; Golebiowski, Jérôme ; Antonczak, Serge ; Fiorucci, Sébastien ; Nguyen, Elizabeth ; Meiler, Jens ; Gutcaits, Aleksandrs ; Marti-Solano, Maria ; Pastor, Manuel ; Selent, Jana ; Stevens, Raymond C. ; Abagyan, Ruben. / Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment : meeting new challenges. In: Structure. 2014 ; Vol. 22, No. 8. pp. 1120-1139.
Bibtex
@article{9eddf8de16224a1cb3b0337062f4a99b,
title = "Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment: meeting new challenges",
abstract = "Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand docking for GPCRs. The four targets in the present third assessment round presented new and diverse challenges for modelers, including prediction of allosteric ligand interaction and activation states in 5-hydroxytryptamine receptors 1B and 2B, and modeling by extremely distant homology for smoothened receptor. Forty-four modeling groups participated in the assessment. State-of-the-art modeling approaches achieved close-to-experimental accuracy for small rigid orthosteric ligands and models built by close homology, and they correctly predicted protein fold for distant homology targets. Predictions of long loops and GPCR activation states remain unsolved problems.",
author = "Irina Kufareva and Vsevolod Katritch and Phil Biggin and Minsup Kim and Kichul Park and Jung, {Sang Won} and Cho, {Art E.} and Sands, {Zara A.} and Liliana Ostopovici-Halip and Bologa, {Cristian G.} and Christoffer Norn and Michal Brylinski and Jeffrey Skolnick and Henrik Ker{\"a}nen and Lenselink, {Bart E.} and {Van Westen}, Gerard and Overington, {John P.} and {De Ter{\'a}{\'a}n}, {Hugo Guti{\'e}rrez} and Vignir Isberg and Fidom, {Kimberley M.} and Lehto, {Thomas M.} and Gloriam, {David E.} and Anirban Ghosh and Uddhavesh Sonavane and Rajendra Joshi and Jie Xia and Hsieh, {Jui Hua} and Liangren Zhang and Wang, {Xiang Simon} and Horst Vogel and Shuguang Yuan and X. Feng and M. Chen and J. Ambia and P. Barth and C{\'e}dric Gageat and Michal Stepniewski and Henri Xhaard and Sebastian Kelm and Pitt, {William R.} and Jiye Shi and Adrien Larsen and Hubert Li and Jeffrey Wagner and Supriyo Bhattacharya and Nagarajan Vaidehi and Kazuhiko Kanou and Vaclav Cvicek and Kim, {Soo Kyung} and Bartosz Trzaskowski and Goddard, {William A.} and Ravinder Abrol and Balaji Selvam and Tikhonova, {Irina G.} and Alberto Cuzzolin and Davide Sabbadin and Antonella Ciancetta and Stefano Moro and Thibaud Freyd and Mari Gabrielsen and Kurt Kristiansen and Ingebrigt Sylte and Gaffney, {Kevin J.} and Petasis, {Nicos A.} and Dorota Latek and Marek Bajda and Krzysztof M{\l}ynarczyk and S{\l}awomir Filipek and Laura L{\'o}pez and Michael Kuiper and Thijs Beuming and Perez-Aguilar, {Jose Manuel} and Wang, {Ray Yu Ruei} and Hahnbeom Park and Per Greisen and Yifan Song and Frank DiMaio and David Baker and Shin, {Woong Hee} and Lim Heo and Lee, {Gyu Rie} and Chaok Seok and Jianyi Yang and Yang Zhang and Marco Ponassi and Camillo Rosano and Georgy Cheremovskiy and Sergei Grudinin and Rajan Chaudhari and Heim, {Andrew J.} and Zhijun Li and Qiang Lv and Grigorov, {Martin G.} and Xin Hu and Hongmao Sun and Min Shen and Noel Southall and Ajit Jadhav and David Rodr{\'i}guez and Anirudh Ranganathan and Jens Carlsson and Rafael Najmanovich and Serdar Durdagi and {De March}, Claire and Julien Diharce and J{\'e}r{\^o}me Golebiowski and Serge Antonczak and S{\'e}bastien Fiorucci and Elizabeth Nguyen and Jens Meiler and Aleksandrs Gutcaits and Maria Marti-Solano and Manuel Pastor and Jana Selent and Stevens, {Raymond C.} and Ruben Abagyan",
year = "2014",
doi = "10.1016/j.str.2014.06.012",
language = "English",
volume = "22",
pages = "1120--1139",
journal = "Structure",
issn = "0969-2126",
publisher = "Cell Press",
number = "8",
}
RIS
TY - JOUR
T1 - Advances in GPCR modeling evaluated by the GPCR Dock 2013 assessment
T2 - meeting new challenges
AU - Kufareva, Irina
AU - Katritch, Vsevolod
AU - Biggin, Phil
AU - Kim, Minsup
AU - Park, Kichul
AU - Jung, Sang Won
AU - Cho, Art E.
AU - Sands, Zara A.
AU - Ostopovici-Halip, Liliana
AU - Bologa, Cristian G.
AU - Norn, Christoffer
AU - Brylinski, Michal
AU - Skolnick, Jeffrey
AU - Keränen, Henrik
AU - Lenselink, Bart E.
AU - Van Westen, Gerard
AU - Overington, John P.
AU - De Teráán, Hugo Gutiérrez
AU - Isberg, Vignir
AU - Fidom, Kimberley M.
AU - Lehto, Thomas M.
AU - Gloriam, David E.
AU - Ghosh, Anirban
AU - Sonavane, Uddhavesh
AU - Joshi, Rajendra
AU - Xia, Jie
AU - Hsieh, Jui Hua
AU - Zhang, Liangren
AU - Wang, Xiang Simon
AU - Vogel, Horst
AU - Yuan, Shuguang
AU - Feng, X.
AU - Chen, M.
AU - Ambia, J.
AU - Barth, P.
AU - Gageat, Cédric
AU - Stepniewski, Michal
AU - Xhaard, Henri
AU - Kelm, Sebastian
AU - Pitt, William R.
AU - Shi, Jiye
AU - Larsen, Adrien
AU - Li, Hubert
AU - Wagner, Jeffrey
AU - Bhattacharya, Supriyo
AU - Vaidehi, Nagarajan
AU - Kanou, Kazuhiko
AU - Cvicek, Vaclav
AU - Kim, Soo Kyung
AU - Trzaskowski, Bartosz
AU - Goddard, William A.
AU - Abrol, Ravinder
AU - Selvam, Balaji
AU - Tikhonova, Irina G.
AU - Cuzzolin, Alberto
AU - Sabbadin, Davide
AU - Ciancetta, Antonella
AU - Moro, Stefano
AU - Freyd, Thibaud
AU - Gabrielsen, Mari
AU - Kristiansen, Kurt
AU - Sylte, Ingebrigt
AU - Gaffney, Kevin J.
AU - Petasis, Nicos A.
AU - Latek, Dorota
AU - Bajda, Marek
AU - Młynarczyk, Krzysztof
AU - Filipek, Sławomir
AU - López, Laura
AU - Kuiper, Michael
AU - Beuming, Thijs
AU - Perez-Aguilar, Jose Manuel
AU - Wang, Ray Yu Ruei
AU - Park, Hahnbeom
AU - Greisen, Per
AU - Song, Yifan
AU - DiMaio, Frank
AU - Baker, David
AU - Shin, Woong Hee
AU - Heo, Lim
AU - Lee, Gyu Rie
AU - Seok, Chaok
AU - Yang, Jianyi
AU - Zhang, Yang
AU - Ponassi, Marco
AU - Rosano, Camillo
AU - Cheremovskiy, Georgy
AU - Grudinin, Sergei
AU - Chaudhari, Rajan
AU - Heim, Andrew J.
AU - Li, Zhijun
AU - Lv, Qiang
AU - Grigorov, Martin G.
AU - Hu, Xin
AU - Sun, Hongmao
AU - Shen, Min
AU - Southall, Noel
AU - Jadhav, Ajit
AU - Rodríguez, David
AU - Ranganathan, Anirudh
AU - Carlsson, Jens
AU - Najmanovich, Rafael
AU - Durdagi, Serdar
AU - De March, Claire
AU - Diharce, Julien
AU - Golebiowski, Jérôme
AU - Antonczak, Serge
AU - Fiorucci, Sébastien
AU - Nguyen, Elizabeth
AU - Meiler, Jens
AU - Gutcaits, Aleksandrs
AU - Marti-Solano, Maria
AU - Pastor, Manuel
AU - Selent, Jana
AU - Stevens, Raymond C.
AU - Abagyan, Ruben
PY - 2014
Y1 - 2014
N2 - Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand docking for GPCRs. The four targets in the present third assessment round presented new and diverse challenges for modelers, including prediction of allosteric ligand interaction and activation states in 5-hydroxytryptamine receptors 1B and 2B, and modeling by extremely distant homology for smoothened receptor. Forty-four modeling groups participated in the assessment. State-of-the-art modeling approaches achieved close-to-experimental accuracy for small rigid orthosteric ligands and models built by close homology, and they correctly predicted protein fold for distant homology targets. Predictions of long loops and GPCR activation states remain unsolved problems.
AB - Despite tremendous successes of GPCR crystallography, the receptors with available structures represent only a small fraction of human GPCRs. An important role of the modeling community is to maximize structural insights for the remaining receptors and complexes. The community-wide GPCR Dock assessment was established to stimulate and monitor the progress in molecular modeling and ligand docking for GPCRs. The four targets in the present third assessment round presented new and diverse challenges for modelers, including prediction of allosteric ligand interaction and activation states in 5-hydroxytryptamine receptors 1B and 2B, and modeling by extremely distant homology for smoothened receptor. Forty-four modeling groups participated in the assessment. State-of-the-art modeling approaches achieved close-to-experimental accuracy for small rigid orthosteric ligands and models built by close homology, and they correctly predicted protein fold for distant homology targets. Predictions of long loops and GPCR activation states remain unsolved problems.
UR - http://www.scopus.com/inward/record.url?scp=84905732337&partnerID=8YFLogxK
U2 - 10.1016/j.str.2014.06.012
DO - 10.1016/j.str.2014.06.012
M3 - Journal article
C2 - 25066135
AN - SCOPUS:84905732337
VL - 22
SP - 1120
EP - 1139
JO - Structure
JF - Structure
SN - 0969-2126
IS - 8
ER -
