Protein target highlights in <scp>CASP15</scp>: Analysis of models by structure providers-Reference-Cited by-同舟云学术

Protein target highlights in CASP15: Analysis of models by structure providers

Published:2023-07-26 Issue:12 Volume:91 Page:1571-1599
ISSN:0887-3585
Container-title:Proteins: Structure, Function, and Bioinformatics
language:en
Short-container-title:Proteins

Author:

Alexander Leila T.¹²^ORCID,Durairaj Janani¹²^ORCID,Kryshtafovych Andriy³^ORCID,Abriata Luciano A.⁴^ORCID,Bayo Yusupha⁵⁶,Bhabha Gira⁷^ORCID,Breyton Cécile⁸^ORCID,Caulton Simon G.⁹^ORCID,Chen James⁷^ORCID,Degroux Séraphine⁸^ORCID,Ekiert Damian C.⁷¹⁰^ORCID,Erlandsen Benedikte S.¹¹^ORCID,Freddolino Peter L.¹²^ORCID,Gilzer Dominic¹³^ORCID,Greening Chris¹⁴¹⁵¹⁶¹⁷^ORCID,Grimes Jonathan M.¹⁸^ORCID,Grinter Rhys¹⁴¹⁹^ORCID,Gurusaran Manickam¹¹^ORCID,Hartmann Marcus D.²⁰²¹^ORCID,Hitchman Charlie J.²²,Keown Jeremy R.¹⁸^ORCID,Kropp Ashleigh¹⁴^ORCID,Kursula Petri²³²⁴^ORCID,Lovering Andrew L.⁹^ORCID,Lemaitre Bruno⁴^ORCID,Lia Andrea²²²⁵^ORCID,Liu Shiheng²⁶²⁷^ORCID,Logotheti Maria²⁰²¹^ORCID,Lu Shuze²⁸,Markússon Sigurbjörn²³^ORCID,Miller Mitchell D.²⁹^ORCID,Minasov George³⁰^ORCID,Niemann Hartmut H.¹³^ORCID,Opazo Felipe³¹³²³³^ORCID,Phillips George N.²⁹³⁴^ORCID,Davies Owen R.¹¹^ORCID,Rommelaere Samuel⁴^ORCID,Rosas‐Lemus Monica³⁰^ORCID,Roversi Pietro⁶²²^ORCID,Satchell Karla³⁰^ORCID,Smith Nathan³⁵,Wilson Mark A.³⁵^ORCID,Wu Kuan‐Lin³⁴^ORCID,Xia Xian²⁶²⁷^ORCID,Xiao Han²⁹³⁴³⁶^ORCID,Zhang Wenhua²⁸^ORCID,Zhou Z. Hong²⁶²⁷^ORCID,Fidelis Krzysztof³^ORCID,Topf Maya³⁷³⁸^ORCID,Moult John³⁹^ORCID,Schwede Torsten¹²^ORCID

Affiliation:

1. Biozentrum University of Basel Basel Switzerland

2. Computational Structural Biology SIB Swiss Institute of Bioinformatics Basel Switzerland

3. Genome Center University of California, Davis Davis California USA

4. School of Life Sciences École Polytechnique Fédérale de Lausanne Lausanne Switzerland

5. Department of Biosciences University of Milano Milan Italy

6. IBBA‐CNR Unit of Milano Institute of Agricultural Biology and Biotechnology Milan Italy

7. Department of Cell Biology New York University School of Medicine New York New York USA

8. Univ. Grenoble Alpes, CNRS, CEA, IBS Grenoble France

9. The University of Birmingham Birmingham UK

10. Department of Microbiology New York University School of Medicine New York New York USA

11. Wellcome Centre for Cell Biology Institute of Cell Biology, University of Edinburgh Edinburgh UK

12. Department of Biological Chemistry, Computational Medicine and Bioinformatics University of Michigan Ann Arbor Michigan USA

13. Department of Chemistry Bielefeld University Bielefeld Germany

14. Department of Microbiology, Biomedicine Discovery Institute Monash University Clayton Victoria Australia

15. Securing Antarctica's Environmental Future Monash University Clayton Victoria Australia

16. Centre to Impact AMR Monash University Clayton Victoria Australia

17. ARC Research Hub for Carbon Utilisation and Recycling Monash University Clayton Victoria Australia

18. Division of Structural Biology, Wellcome Centre for Human Genetics University of Oxford Oxford UK

19. Centre for Electron Microscopy of Membrane Proteins Monash Institute of Pharmaceutical Sciences Parkville Victoria Australia

20. Max Planck Institute for Biology Tübingen Germany

21. Interfaculty Institute of Biochemistry, University of Tübingen Tübingen Germany

22. Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology University of Leicester Leicester UK

23. Department of Biomedicine University of Bergen Bergen Norway

24. Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu University of Oulu Oulu Finland

25. ISPA‐CNR Unit of Lecce Institute of Sciences of Food Production Lecce Italy

26. Department of Microbiology, Immunology, and Molecular Genetics University of California Los Angeles California USA

27. California NanoSystems Institute University of California Los Angeles California USA

28. Lanzhou University School of Life Sciences Lanzhou China

29. Department of Biosciences Rice University Houston Texas USA

30. Department of Microbiology‐Immunology Northwestern Feinberg School of Medicine Chicago Illinois USA

31. NanoTag Biotechnologies GmbH Göttingen Germany

32. Institute of Neuro‐ and Sensory Physiology University of Göttingen Medical Center Göttingen Germany

33. Center for Biostructural Imaging of Neurodegeneration (BIN) University of Göttingen Medical Center Göttingen Germany

34. Department of Chemistry Rice University Houston Texas USA

35. Department of Biochemistry and the Redox Biology Center University of Nebraska Lincoln Nebraska USA

36. Department of Bioengineering Rice University Houston Texas USA

37. University Medical Center Hamburg‐Eppendorf (UKE) Hamburg Germany

38. Centre for Structural Systems Biology Leibniz‐Institut für Virologie (LIV) Hamburg Germany

39. Department of Cell Biology and Molecular Genetics, Institute for Bioscience and Biotechnology Research University of Maryland Rockville Maryland USA

Abstract

AbstractWe present an in‐depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three‐dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

Funder

Australian Research Council

Cancer Prevention and Research Institute of Texas

Fundamental Research Funds for the Central Universities

Jane Coffin Childs Memorial Fund for Medical Research

National Health and Medical Research Council

National Institutes of Health

National Natural Science Foundation of China

National Science Foundation

Pew Charitable Trusts

Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung

Welch Foundation