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

Author:

Lensink Marc F.1ORCID,Velankar Sameer2,Kryshtafovych Andriy3,Huang Shen‐You4,Schneidman‐Duhovny Dina56,Sali Andrej567,Segura Joan8,Fernandez‐Fuentes Narcis9,Viswanath Shruthi1011,Elber Ron1112,Grudinin Sergei1314,Popov Petr131415,Neveu Emilie1314,Lee Hasup16,Baek Minkyung16,Park Sangwoo16,Heo Lim16,Rie Lee Gyu16,Seok Chaok16,Qin Sanbo17,Zhou Huan‐Xiang17,Ritchie David W.18,Maigret Bernard19,Devignes Marie‐Dominique19,Ghoorah Anisah20,Torchala Mieczyslaw21,Chaleil Raphaël A.G.21,Bates Paul A.21,Ben‐Zeev Efrat22,Eisenstein Miriam23,Negi Surendra S.24,Weng Zhiping25,Vreven Thom25,Pierce Brian G.25,Borrman Tyler M.25,Yu Jinchao26,Ochsenbein Françoise26,Guerois Raphaël26,Vangone Anna27,Rodrigues João P.G.L.M.27,van Zundert Gydo27,Nellen Mehdi27,Xue Li27,Karaca Ezgi27,Melquiond Adrien S.J.27,Visscher Koen27,Kastritis Panagiotis L.27,Bonvin Alexandre M.J.J.27ORCID,Xu Xianjin28,Qiu Liming28,Yan Chengfei2829,Li Jilong30,Ma Zhiwei2829,Cheng Jianlin3031,Zou Xiaoqin28293132,Shen Yang33ORCID,Peterson Lenna X.34,Kim Hyung‐Rae34,Roy Amit3435,Han Xusi34,Esquivel‐Rodriguez Juan36,Kihara Daisuke3436,Yu Xiaofeng37,Bruce Neil J.37,Fuller Jonathan C.37,Wade Rebecca C.373839,Anishchenko Ivan40,Kundrotas Petras J.40,Vakser Ilya A.4041,Imai Kenichiro42,Yamada Kazunori42,Oda Toshiyuki42,Nakamura Tsukasa43,Tomii Kentaro4243,Pallara Chiara44,Romero‐Durana Miguel44,Jiménez‐García Brian44,Moal Iain H.44,Férnandez‐Recio Juan44,Joung Jong Young45,Kim Jong Yun45,Joo Keehyoung4546,Lee Jooyoung4547,Kozakov Dima48,Vajda Sandor4849,Mottarella Scott48,Hall David R.48,Beglov Dmitri48,Mamonov Artem48,Xia Bing48,Bohnuud Tanggis48,Del Carpio Carlos A.5051,Ichiishi Eichiro52,Marze Nicholas53,Kuroda Daisuke53,Roy Burman Shourya S.53,Gray Jeffrey J.5354ORCID,Chermak Edrisse55,Cavallo Luigi55,Oliva Romina56,Tovchigrechko Andrey57,Wodak Shoshana J.5859

Affiliation:

1. University LilleCNRS UMR8576 UGSFLilleF‐59000 France

2. European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)Wellcome Trust Genome CampusHinxton CambridgeCB10 1SD United Kingdom

3. Genome CenterUniversity of CaliforniaDavis California95616

4. Research Support Computing, University of Missouri Bioinformatics Consortium, and Department of Computer Science, University of Missouri Columbia Missouri65211

5. Department of Bioengineering and Therapeutic SciencesUniversity of California San FranciscoSan Francisco California94158

6. Department of Pharmaceutical ChemistryUniversity of California San FranciscoSan Francisco California94158

7. California Institute for Quantitative Biosciences (QB3)University of California San FranciscoSan Francisco California94158

8. GN7 of the National Institute for Bioinformatics (INB) and Biocomputing Unit, National Center of Biotechnology (CSIC)Madrid28049 Spain

9. Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth UniversityAberystwythSY233FG United Kingdom

10. Department of Computer ScienceUniversity of Texas at AustinAustin Texas78712

11. Institute for Computational Engineering and Sciences, University of Texas at AustinAustin Texas78712

12. Department of ChemistryUniversity of Texas at AustinAustin Texas78712

13. LJK, University Grenoble Alpes, CNRSGrenoble38000 France

14. INRIAGrenoble38000 France

15. Moscow Institute of Physics and TechnologyDolgoprudniy Russia

16. Department of ChemistrySeoul National UniversitySeoul151‐747 Republic of Korea

17. Department of Physics and Institute of Molecular BiophysicsFlorida State UniversityTallahassee Florida32306 USA

18. INRIA Nancy—Grand EstVillers‐lès‐Nancy54600 France

19. CNRS, LORIACampus Scientifique, BP 239Vandœuvre‐lès‐Nancy54506 France

20. Department of Computer Science and EngineeringUniversity of MauritiusReduit Mauritius

21. Biomolecular Modelling Laboratory, the Francis Crick Institute, Lincoln's Inn Fields LaboratoryLondonWC2A 3LY United Kingdom

22. G‐INCPM, Weizmann Institute of ScienceRehovot7610001 Israel

23. Department of Chemical Research SupportWeizmann Institute of ScienceRehovot7610001 Israel

24. Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch301 University BoulevardGalveston Texas77555‐0857

25. Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical SchoolWorcester Massachusetts01605

26. Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Saclay, CEA‐SaclayGif‐sur‐Yvette91191 France

27. Bijvoet Center for Biomolecular Research, Faculty of Science – Chemistry, Utrecht UniversityPadualaan 8Utrecht3584 CH The Netherlands

28. Dalton Cardiovascular Research Center, University of MissouriColumbia Missouri65211

29. Department of Physics and AstronomyUniversity of MissouriColumbia Missouri65211

30. Department of Computer ScienceUniversity of MissouriColumbia Missouri65211

31. Informatics Institute, University of MissouriColumbia Missouri65211

32. Department of BiochemistryUniversity of MissouriColumbia Missouri65211

33. Toyota Technological Institute at Chicago6045 S Kenwood AvenueChicago Illinois60637

34. Department of Biological SciencesPurdue UniversityWest Lafayette Indiana47907

35. Bioinformatics and Computational Biosciences Branch, Rocky Mountain Laboratories, National Institutes of HealthHamilton Montano 59840

36. Department of Computer SciencePurdue UniversityWest Lafayette IN USA 47907

37. Molecular and Cellular Modeling GroupHeidelberg Institute for Theoretical Studies (HITS)Heidelberg Germany

38. Center for Molecular Biology (ZMBH), DKFZ‐ZMBH Alliance, Heidelberg UniversityHeidelberg Germany

39. Interdisciplinary Center for Scientific Computing (IWR), Heidelberg UniversityHeidelberg Germany

40. Center for Computational Biology, The University of KansasLawrence Kansas66047

41. Department of Molecular BiosciencesThe University of KansasLawrence Kansas66047

42. Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)Koto‐Ku Japan

43. Graduate School of Frontier Sciencesthe University of TokyoKashiwa Japan

44. Joint BSC‐CRG‐IRB Research Program in Computational Biology, Barcelona Supercomputing CenterC/Jordi Girona 29Barcelona08034 Spain

45. Center for in‐Silico Protein Science, Korea Institute for Advanced StudySeoul130‐722Korea

46. Center for Advanced Computation, Korea Institute for Advanced StudySeoul130‐722Korea

47. School of Computational ScienceKorea Institute for Advanced StudySeoul130‐722Korea

48. Department of Biomedical EngineeringBoston UniversityBoston Massachusetts

49. Department of ChemistryBoston UniversityBoston Massachusetts

50. Institute of Biological Diversity, International Pacific Institute of IndianaBloomington Indiana47401

51. Drosophila Genetic Resource Center, Kyoto Institute of TechnologyUkyo‐Ku616‐8354 Japan

52. International University of Health and Welfare Hospital (IUHW Hospital)Asushiobara‐City, Tochigi Prefecture329‐2763 Japan

53. Department of Chemical and Biomolecular EngineeringJohns Hopkins UniversityBaltimore Maryland21218

54. Program in Molecular Biophysics, Johns Hopkins UniversityBaltimore Maryland21218

55. King Abdullah University of Science and Technology Saudi Arabia

56. University of Naples “Parthenope” Napoli Italy

57. J. Craig Venter Institute9704 Medical Center DriveRockville Maryland20850

58. Departments of Biochemistry and Molecular GeneticsUniversity of TorontoToronto Ontario Canada

59. VIB Structural Biology Research CenterVUB Pleinlaan 2Brussels1050 Belgium

Funder

NIH

Biotechnology and Biological Sciences Research Council

Research Councils UK Academic Fellowship program

Cancer Research UK

Klaus Tschira Foundation

Platform Project for Supporting in Drug Discovery and Life Science Research

Japan Agency for Medical Research and Development

Agence Nationale de la Recherche

National Research Foundation of Korea (NRF)

BIP

H2020 Marie Sklodowska-Curie Individual Fellowship

Netherlands Organization for Scientific Research Veni

National Science Foundation

EU

BMBF

Spanish Ministry of Economy and Competitiveness

European Union

National Institute of Supercomputing and Networking

US-Israel BSF

Regione Campania

Publisher

Wiley

Subject

Molecular Biology,Biochemistry,Structural Biology

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