Skip to main page content
Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2019 Dec;87(12):1200-1221.
doi: 10.1002/prot.25838. Epub 2019 Oct 25.

Blind Prediction of Homo- And Hetero-Protein Complexes: The CASP13-CAPRI Experiment

Marc F Lensink  1 Guillaume Brysbaert  1 Nurul Nadzirin  2 Sameer Velankar  2 Raphaël A G Chaleil  3 Tereza Gerguri  3 Paul A Bates  3 Elodie Laine  4 Alessandra Carbone  4   5 Sergei Grudinin  6 Ren Kong  7 Ran-Ran Liu  7 Xi-Ming Xu  7 Hang Shi  7 Shan Chang  7 Miriam Eisenstein  8 Agnieszka Karczynska  9 Cezary Czaplewski  9 Emilia Lubecka  10 Agnieszka Lipska  9 Paweł Krupa  11 Magdalena Mozolewska  12 Łukasz Golon  9 Sergey Samsonov  9 Adam Liwo  9   13 Silvia Crivelli  14 Guillaume Pagès  6 Mikhail Karasikov  15 Maria Kadukova  6   16 Yumeng Yan  17 Sheng-You Huang  17 Mireia Rosell  18   19 Luis A Rodríguez-Lumbreras  18   19 Miguel Romero-Durana  18 Lucía Díaz-Bueno  18 Juan Fernandez-Recio  18   19   20 Charles Christoffer  21 Genki Terashi  22 Woong-Hee Shin  22 Tunde Aderinwale  21 Sai Raghavendra Maddhuri Venkata Subraman  21 Daisuke Kihara  21 Dima Kozakov  23 Sandor Vajda  24   25 Kathryn Porter  24 Dzmitry Padhorny  23 Israel Desta  24 Dmitri Beglov  24 Mikhail Ignatov  23 Sergey Kotelnikov  16   23 Iain H Moal  2 David W Ritchie  26 Isaure Chauvot de Beauchêne  26 Bernard Maigret  26 Marie-Dominique Devignes  26 Maria E Ruiz Echartea  26 Didier Barradas-Bautista  27 Zhen Cao  27 Luigi Cavallo  27 Romina Oliva  28 Yue Cao  29 Yang Shen  29 Minkyung Baek  30 Taeyong Park  30 Hyeonuk Woo  30 Chaok Seok  30 Merav Braitbard  31 Lirane Bitton  32 Dina Scheidman-Duhovny  31   32 Justas Dapkūnas  33 Kliment Olechnovič  33 Česlovas Venclovas  33 Petras J Kundrotas  34 Saveliy Belkin  34 Devlina Chakravarty  34 Varsha D Badal  34 Ilya A Vakser  34 Thom Vreven  35 Sweta Vangaveti  35 Tyler Borrman  35 Zhiping Weng  35 Johnathan D Guest  36   37 Ragul Gowthaman  36   37 Brian G Pierce  36   37 Xianjin Xu  38 Rui Duan  38 Liming Qiu  38 Jie Hou  39 Benjamin Ryan Merideth  38   40 Zhiwei Ma  38   41 Jianlin Cheng  39   40 Xiaoqin Zou  38   40   41   42 Panagiotis I Koukos  43 Jorge Roel-Touris  43 Francesco Ambrosetti  43 Cunliang Geng  43 Jörg Schaarschmidt  43 Mikael E Trellet  43 Adrien S J Melquiond  43 Li Xue  43 Brian Jiménez-García  43 Charlotte W van Noort  43 Rodrigo V Honorato  43 Alexandre M J J Bonvin  43 Shoshana J Wodak  44
Affiliations

Blind Prediction of Homo- And Hetero-Protein Complexes: The CASP13-CAPRI Experiment

Marc F Lensink et al. Proteins. .

Abstract

We present the results for CAPRI Round 46, the third joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of 20 targets including 14 homo-oligomers and 6 heterocomplexes. Eight of the homo-oligomer targets and one heterodimer comprised proteins that could be readily modeled using templates from the Protein Data Bank, often available for the full assembly. The remaining 11 targets comprised 5 homodimers, 3 heterodimers, and two higher-order assemblies. These were more difficult to model, as their prediction mainly involved "ab-initio" docking of subunit models derived from distantly related templates. A total of ~30 CAPRI groups, including 9 automatic servers, submitted on average ~2000 models per target. About 17 groups participated in the CAPRI scoring rounds, offered for most targets, submitting ~170 models per target. The prediction performance, measured by the fraction of models of acceptable quality or higher submitted across all predictors groups, was very good to excellent for the nine easy targets. Poorer performance was achieved by predictors for the 11 difficult targets, with medium and high quality models submitted for only 3 of these targets. A similar performance "gap" was displayed by scorer groups, highlighting yet again the unmet challenge of modeling the conformational changes of the protein components that occur upon binding or that must be accounted for in template-based modeling. Our analysis also indicates that residues in binding interfaces were less well predicted in this set of targets than in previous Rounds, providing useful insights for directions of future improvements.

Keywords: CAPRI; CASP; blind prediction; docking; oligomeric state; protein assemblies; protein complexes; protein-protein interaction; template-based modeling.

Similar articles

  • The challenge of modeling protein assemblies: the CASP12-CAPRI experiment.
    Lensink MF, Velankar S, Baek M, Heo L, Seok C, Wodak SJ. Lensink MF, et al. Proteins. 2018 Mar;86 Suppl 1:257-273. doi: 10.1002/prot.25419. Epub 2017 Nov 26. Proteins. 2018. PMID: 29127686
  • Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.
    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 RA, 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 JP, van Zundert G, Nellen M, Xue L, Karaca E, Melquiond AS, Visscher K, Kastritis PL, Bonvin AM, 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. Lensink MF, et al. Version 2. Proteins. 2016 Sep;84 Suppl 1(Suppl Suppl 1):323-48. doi: 10.1002/prot.25007. Epub 2016 Jun 1. Proteins. 2016. PMID: 27122118 Free PMC article.
  • Template-based modeling and ab-initio docking using CoDock in CAPRI.
    Kong R, Liu RR, Xu XM, Zhang DW, Xu XS, Shi H, Chang S. Kong R, et al. Proteins. 2020 Mar 17. doi: 10.1002/prot.25892. Online ahead of print. Proteins. 2020. PMID: 32181952
  • What method to use for protein-protein docking?
    Porter KA, Desta I, Kozakov D, Vajda S. Porter KA, et al. Curr Opin Struct Biol. 2019 Apr;55:1-7. doi: 10.1016/j.sbi.2018.12.010. Epub 2019 Feb 1. Curr Opin Struct Biol. 2019. PMID: 30711743 Free PMC article. Review.
  • Protein-protein docking tested in blind predictions: the CAPRI experiment.
    Janin J. Janin J. Mol Biosyst. 2010 Dec;6(12):2351-62. doi: 10.1039/c005060c. Epub 2010 Aug 19. Mol Biosyst. 2010. PMID: 20725658 Review.
See all similar articles

Cited by 1 article

References

REFERENCES

    1. Ideker T, Sharan R. Protein networks in disease. Genome Res. 2008;18(4):644-652.
    1. Barabasi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011;12(1):56-68.
    1. Berman HM, Battistuz T, Bhat TN, et al. The protein data bank. Acta Crystallogr Sect D: Biol Crystallogr. 2002;58(1):899-907.
    1. Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol. 1999;285(5):2177-2198.
    1. Dey S, Pal A, Chakrabarti P, Janin J. The subunit interfaces of weakly associated homodimeric proteins. J Mol Biol. 2010;398(1):146-160.

Publication types

LinkOut - more resources

Feedback