Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment

Marc F. Lensink, Sameer Velankar, Andriy Kryshtafovych, Shen You Huang, Dina Schneidman-Duhovny, Andrej Sali, Joan Segura, Narcis Fernandez-Fuentes, Shruthi Viswanath, Ron Elber, Sergei Grudinin, Petr Popov, Emilie Neveu, Hasup Lee, Minkyung Baek, Sangwoo Park, Lim Heo, Gyu Rie Lee, Chaok Seok, Sanbo QinHuan Xiang Zhou, David W. Ritchie, Bernard Maigret, Marie Dominique Devignes, Anisah Ghoorah, Mieczyslaw Torchala, Raphaël A G Chaleil, Paul A. Bates, Efrat Ben-Zeev, Miriam Eisenstein, Surendra S. Negi, Zhiping Weng, Thom Vreven, Brian G. Pierce, Tyler M. Borrman, Jinchao Yu, Françoise Ochsenbein, Raphaël Guerois, Anna Vangone, João P G L M Rodrigues, Gydo van Zundert, Mehdi Nellen, Li Xue, Ezgi Karaca, Adrien S J Melquiond, Koen Visscher, Panagiotis L. Kastritis, Alexandre M J J Bonvin, Xianjin Xu, Liming Qiu, Chengfei Yan, Jilong Li, Zhiwei Ma, Jianlin Cheng, Xiaoqin Zou, Yang Shen, Lenna X. Peterson, Hyung Rae Kim, Amit Roy, Xusi Han, Juan Esquivel-Rodriguez, Daisuke Kihara, Xiaofeng Yu, Neil J. Bruce, Jonathan C. Fuller, Rebecca C. Wade, Ivan Anishchenko, Petras J. Kundrotas, Ilya A. Vakser, Kenichiro Imai, Kazunori Yamada, Toshiyuki Oda, Tsukasa Nakamura, Kentaro Tomii, Chiara Pallara, Miguel Romero-Durana, Brian Jiménez-García, Iain H. Moal, Juan Férnandez-Recio, Jong Young Joung, Jong Yun Kim, Keehyoung Joo, Jooyoung Lee, Dima Kozakov, Sandor Vajda, Scott Mottarella, David R. Hall, Dmitri Beglov, Artem Mamonov, Bing Xia, Tanggis Bohnuud, Carlos A. Del Carpio, Eichiro Ichiishi, Nicholas Marze, Daisuke Kuroda, Shourya S. Roy Burman, Jeffrey J Gray, Edrisse Chermak, Luigi Cavallo, Romina Oliva, Andrey Tovchigrechko, Shoshana J. Wodak

Research output: Contribution to journalArticle

Abstract

We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.

Original languageEnglish (US)
JournalProteins: Structure, Function and Genetics
DOIs
StateAccepted/In press - 2016

Fingerprint

Proteins
Experiments
State assignment
Joints
Databases
Crystals

Keywords

  • Blind prediction
  • CAPRI
  • CASP
  • Oligomer state
  • Protein docking
  • Protein interaction

ASJC Scopus subject areas

  • Biochemistry
  • Structural Biology
  • Molecular Biology

Cite this

Lensink, M. F., Velankar, S., Kryshtafovych, A., Huang, S. Y., Schneidman-Duhovny, D., Sali, A., ... Wodak, S. J. (Accepted/In press). Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment. Proteins: Structure, Function and Genetics. https://doi.org/10.1002/prot.25007

Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling : A CASP-CAPRI experiment. / Lensink, Marc F.; Velankar, Sameer; Kryshtafovych, Andriy; Huang, Shen You; Schneidman-Duhovny, Dina; Sali, Andrej; Segura, Joan; Fernandez-Fuentes, Narcis; Viswanath, Shruthi; Elber, Ron; Grudinin, Sergei; Popov, Petr; Neveu, Emilie; Lee, Hasup; Baek, Minkyung; Park, Sangwoo; Heo, Lim; Rie Lee, Gyu; Seok, Chaok; Qin, Sanbo; Zhou, Huan Xiang; Ritchie, David W.; Maigret, Bernard; Devignes, Marie Dominique; Ghoorah, Anisah; Torchala, Mieczyslaw; Chaleil, Raphaël A G; Bates, Paul A.; Ben-Zeev, Efrat; Eisenstein, Miriam; Negi, Surendra S.; Weng, Zhiping; Vreven, Thom; Pierce, Brian G.; Borrman, Tyler M.; Yu, Jinchao; Ochsenbein, Françoise; Guerois, Raphaël; Vangone, Anna; Rodrigues, João P G L M; van Zundert, Gydo; Nellen, Mehdi; Xue, Li; Karaca, Ezgi; Melquiond, Adrien S J; Visscher, Koen; Kastritis, Panagiotis L.; Bonvin, Alexandre M J J; Xu, Xianjin; Qiu, Liming; Yan, Chengfei; Li, Jilong; Ma, Zhiwei; Cheng, Jianlin; Zou, Xiaoqin; Shen, Yang; Peterson, Lenna X.; Kim, Hyung Rae; Roy, Amit; Han, Xusi; Esquivel-Rodriguez, Juan; Kihara, Daisuke; Yu, Xiaofeng; Bruce, Neil J.; Fuller, Jonathan C.; Wade, Rebecca C.; Anishchenko, Ivan; Kundrotas, Petras J.; Vakser, Ilya A.; Imai, Kenichiro; Yamada, Kazunori; Oda, Toshiyuki; Nakamura, Tsukasa; Tomii, Kentaro; Pallara, Chiara; Romero-Durana, Miguel; Jiménez-García, Brian; Moal, Iain H.; Férnandez-Recio, Juan; Joung, Jong Young; Kim, Jong Yun; Joo, Keehyoung; Lee, Jooyoung; Kozakov, Dima; Vajda, Sandor; Mottarella, Scott; Hall, David R.; Beglov, Dmitri; Mamonov, Artem; Xia, Bing; Bohnuud, Tanggis; Del Carpio, Carlos A.; Ichiishi, Eichiro; Marze, Nicholas; Kuroda, Daisuke; Roy Burman, Shourya S.; Gray, Jeffrey J; Chermak, Edrisse; Cavallo, Luigi; Oliva, Romina; Tovchigrechko, Andrey; Wodak, Shoshana J.

In: Proteins: Structure, Function and Genetics, 2016.

Research output: Contribution to journalArticle

Lensink, MF, Velankar, S, Kryshtafovych, A, Huang, SY, Schneidman-Duhovny, D, Sali, A, Segura, J, Fernandez-Fuentes, N, Viswanath, S, Elber, R, Grudinin, S, Popov, P, Neveu, E, Lee, H, Baek, M, Park, S, Heo, L, Rie Lee, G, Seok, C, Qin, S, Zhou, HX, Ritchie, DW, Maigret, B, Devignes, MD, Ghoorah, A, Torchala, M, Chaleil, RAG, Bates, PA, Ben-Zeev, E, Eisenstein, M, Negi, SS, Weng, Z, Vreven, T, Pierce, BG, Borrman, TM, Yu, J, Ochsenbein, F, Guerois, R, Vangone, A, Rodrigues, JPGLM, van Zundert, G, Nellen, M, Xue, L, Karaca, E, Melquiond, ASJ, Visscher, K, Kastritis, PL, Bonvin, AMJJ, Xu, X, Qiu, L, Yan, C, Li, J, Ma, Z, Cheng, J, Zou, X, Shen, Y, Peterson, LX, Kim, HR, Roy, A, Han, X, Esquivel-Rodriguez, J, Kihara, D, Yu, X, Bruce, NJ, Fuller, JC, Wade, RC, Anishchenko, I, Kundrotas, PJ, Vakser, IA, Imai, K, Yamada, K, Oda, T, Nakamura, T, Tomii, K, Pallara, C, Romero-Durana, M, Jiménez-García, B, Moal, IH, Férnandez-Recio, J, Joung, JY, Kim, JY, Joo, K, Lee, J, Kozakov, D, Vajda, S, Mottarella, S, Hall, DR, Beglov, D, Mamonov, A, Xia, B, Bohnuud, T, Del Carpio, CA, Ichiishi, E, Marze, N, Kuroda, D, Roy Burman, SS, Gray, JJ, Chermak, E, Cavallo, L, Oliva, R, Tovchigrechko, A & Wodak, SJ 2016, 'Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment', Proteins: Structure, Function and Genetics. https://doi.org/10.1002/prot.25007
Lensink, Marc F. ; Velankar, Sameer ; Kryshtafovych, Andriy ; Huang, Shen You ; Schneidman-Duhovny, Dina ; Sali, Andrej ; Segura, Joan ; Fernandez-Fuentes, Narcis ; Viswanath, Shruthi ; Elber, Ron ; Grudinin, Sergei ; Popov, Petr ; Neveu, Emilie ; Lee, Hasup ; Baek, Minkyung ; Park, Sangwoo ; Heo, Lim ; Rie Lee, Gyu ; Seok, Chaok ; Qin, Sanbo ; Zhou, Huan Xiang ; Ritchie, David W. ; Maigret, Bernard ; Devignes, Marie Dominique ; Ghoorah, Anisah ; Torchala, Mieczyslaw ; Chaleil, Raphaël A G ; Bates, Paul A. ; Ben-Zeev, Efrat ; Eisenstein, Miriam ; Negi, Surendra S. ; Weng, Zhiping ; Vreven, Thom ; Pierce, Brian G. ; Borrman, Tyler M. ; Yu, Jinchao ; Ochsenbein, Françoise ; Guerois, Raphaël ; Vangone, Anna ; Rodrigues, João P G L M ; van Zundert, Gydo ; Nellen, Mehdi ; Xue, Li ; Karaca, Ezgi ; Melquiond, Adrien S J ; Visscher, Koen ; Kastritis, Panagiotis L. ; Bonvin, Alexandre M J J ; Xu, Xianjin ; Qiu, Liming ; Yan, Chengfei ; Li, Jilong ; Ma, Zhiwei ; Cheng, Jianlin ; Zou, Xiaoqin ; Shen, Yang ; Peterson, Lenna X. ; Kim, Hyung Rae ; Roy, Amit ; Han, Xusi ; Esquivel-Rodriguez, Juan ; Kihara, Daisuke ; Yu, Xiaofeng ; Bruce, Neil J. ; Fuller, Jonathan C. ; Wade, Rebecca C. ; Anishchenko, Ivan ; Kundrotas, Petras J. ; Vakser, Ilya A. ; Imai, Kenichiro ; Yamada, Kazunori ; Oda, Toshiyuki ; Nakamura, Tsukasa ; Tomii, Kentaro ; Pallara, Chiara ; Romero-Durana, Miguel ; Jiménez-García, Brian ; Moal, Iain H. ; Férnandez-Recio, Juan ; Joung, Jong Young ; Kim, Jong Yun ; Joo, Keehyoung ; Lee, Jooyoung ; Kozakov, Dima ; Vajda, Sandor ; Mottarella, Scott ; Hall, David R. ; Beglov, Dmitri ; Mamonov, Artem ; Xia, Bing ; Bohnuud, Tanggis ; Del Carpio, Carlos A. ; Ichiishi, Eichiro ; Marze, Nicholas ; Kuroda, Daisuke ; Roy Burman, Shourya S. ; Gray, Jeffrey J ; Chermak, Edrisse ; Cavallo, Luigi ; Oliva, Romina ; Tovchigrechko, Andrey ; Wodak, Shoshana J. / Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling : A CASP-CAPRI experiment. In: Proteins: Structure, Function and Genetics. 2016.
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issn = "0887-3585",
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TY - JOUR

T1 - Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling

T2 - A CASP-CAPRI experiment

AU - Lensink, Marc F.

AU - Velankar, Sameer

AU - Kryshtafovych, Andriy

AU - Huang, Shen You

AU - Schneidman-Duhovny, Dina

AU - Sali, Andrej

AU - Segura, Joan

AU - Fernandez-Fuentes, Narcis

AU - Viswanath, Shruthi

AU - Elber, Ron

AU - Grudinin, Sergei

AU - Popov, Petr

AU - Neveu, Emilie

AU - Lee, Hasup

AU - Baek, Minkyung

AU - Park, Sangwoo

AU - Heo, Lim

AU - Rie Lee, Gyu

AU - Seok, Chaok

AU - Qin, Sanbo

AU - Zhou, Huan Xiang

AU - Ritchie, David W.

AU - Maigret, Bernard

AU - Devignes, Marie Dominique

AU - Ghoorah, Anisah

AU - Torchala, Mieczyslaw

AU - Chaleil, Raphaël A G

AU - Bates, Paul A.

AU - Ben-Zeev, Efrat

AU - Eisenstein, Miriam

AU - Negi, Surendra S.

AU - Weng, Zhiping

AU - Vreven, Thom

AU - Pierce, Brian G.

AU - Borrman, Tyler M.

AU - Yu, Jinchao

AU - Ochsenbein, Françoise

AU - Guerois, Raphaël

AU - Vangone, Anna

AU - Rodrigues, João P G L M

AU - van Zundert, Gydo

AU - Nellen, Mehdi

AU - Xue, Li

AU - Karaca, Ezgi

AU - Melquiond, Adrien S J

AU - Visscher, Koen

AU - Kastritis, Panagiotis L.

AU - Bonvin, Alexandre M J J

AU - Xu, Xianjin

AU - Qiu, Liming

AU - Yan, Chengfei

AU - Li, Jilong

AU - Ma, Zhiwei

AU - Cheng, Jianlin

AU - Zou, Xiaoqin

AU - Shen, Yang

AU - Peterson, Lenna X.

AU - Kim, Hyung Rae

AU - Roy, Amit

AU - Han, Xusi

AU - Esquivel-Rodriguez, Juan

AU - Kihara, Daisuke

AU - Yu, Xiaofeng

AU - Bruce, Neil J.

AU - Fuller, Jonathan C.

AU - Wade, Rebecca C.

AU - Anishchenko, Ivan

AU - Kundrotas, Petras J.

AU - Vakser, Ilya A.

AU - Imai, Kenichiro

AU - Yamada, Kazunori

AU - Oda, Toshiyuki

AU - Nakamura, Tsukasa

AU - Tomii, Kentaro

AU - Pallara, Chiara

AU - Romero-Durana, Miguel

AU - Jiménez-García, Brian

AU - Moal, Iain H.

AU - Férnandez-Recio, Juan

AU - Joung, Jong Young

AU - Kim, Jong Yun

AU - Joo, Keehyoung

AU - Lee, Jooyoung

AU - Kozakov, Dima

AU - Vajda, Sandor

AU - Mottarella, Scott

AU - Hall, David R.

AU - Beglov, Dmitri

AU - Mamonov, Artem

AU - Xia, Bing

AU - Bohnuud, Tanggis

AU - Del Carpio, Carlos A.

AU - Ichiishi, Eichiro

AU - Marze, Nicholas

AU - Kuroda, Daisuke

AU - Roy Burman, Shourya S.

AU - Gray, Jeffrey J

AU - Chermak, Edrisse

AU - Cavallo, Luigi

AU - Oliva, Romina

AU - Tovchigrechko, Andrey

AU - Wodak, Shoshana J.

PY - 2016

Y1 - 2016

N2 - We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.

AB - We present the results for CAPRI Round 30, the first joint CASP-CAPRI experiment, which brought together experts from the protein structure prediction and protein-protein docking communities. The Round comprised 25 targets from amongst those submitted for the CASP11 prediction experiment of 2014. The targets included mostly homodimers, a few homotetramers, and two heterodimers, and comprised protein chains that could readily be modeled using templates from the Protein Data Bank. On average 24 CAPRI groups and 7 CASP groups submitted docking predictions for each target, and 12 CAPRI groups per target participated in the CAPRI scoring experiment. In total more than 9500 models were assessed against the 3D structures of the corresponding target complexes. Results show that the prediction of homodimer assemblies by homology modeling techniques and docking calculations is quite successful for targets featuring large enough subunit interfaces to represent stable associations. Targets with ambiguous or inaccurate oligomeric state assignments, often featuring crystal contact-sized interfaces, represented a confounding factor. For those, a much poorer prediction performance was achieved, while nonetheless often providing helpful clues on the correct oligomeric state of the protein. The prediction performance was very poor for genuine tetrameric targets, where the inaccuracy of the homology-built subunit models and the smaller pair-wise interfaces severely limited the ability to derive the correct assembly mode. Our analysis also shows that docking procedures tend to perform better than standard homology modeling techniques and that highly accurate models of the protein components are not always required to identify their association modes with acceptable accuracy.

KW - Blind prediction

KW - CAPRI

KW - CASP

KW - Oligomer state

KW - Protein docking

KW - Protein interaction

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U2 - 10.1002/prot.25007

DO - 10.1002/prot.25007

M3 - Article

C2 - 27122118

AN - SCOPUS:84973338605

JO - Proteins: Structure, Function and Genetics

JF - Proteins: Structure, Function and Genetics

SN - 0887-3585

ER -