Protein target highlights in CASP15 : Analysis of models by structure providers - Groupe Membrane et pathogènes / Membrane and Pathogens Group (IBS-MP)
Article Dans Une Revue Proteins - Structure, Function and Bioinformatics Année : 2023

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

Leila T. Alexander (1, 2) , Janani Durairaj (1, 2) , Andriy Kryshtafovych (3) , Luciano A. Abriata (4) , Yusupha Bayo (5) , Gira Bhabha (6) , Cécile Breyton (7) , Simon Caulton (8) , James Chen (9) , Séraphine Degroux (7) , Damian Ekiert (6) , Benedikte Erlandsen (10) , Peter Freddolino (11) , Dominic Gilzer (12) , Chris Greening (13) , Jonathan Grimes (14) , Rhys Grinter (15) , Manickam Gurusaran (10) , Marcus Hartmann (16) , Charlie Hitchman (17) , Jeremy Keown (18) , Ashleigh Kropp (15) , Petri Kursula (19, 20) , Andrew Lovering (8) , Bruno Lemaitre (4) , Andrea Lia (17) , Shiheng Liu (21) , Maria Logotheti (16) , Shuze Lu (22) , Sigurbjörn Markússon (20) , Mitchell Miller (23) , George Minasov (24) , Hartmut Niemann (12) , Felipe Opazo (25) , George Phillips (23) , Owen R. Davies (10) , Samuel Rommelaere (4) , Monica Rosas-Lemus (24) , Pietro Roversi (26) , Karla Satchell (24) , Nathan Smith (27) , Mark Wilson (27) , Kuan-Lin Wu (23) , Xian Xia (21) , Han Xiao (23) , Wenhua Zhang (22) , Z. Hong Zhou (21) , Krzysztof Fidelis (28) , Maya Topf (29, 30) , John Moult (31) , Torsten Schwede (1)
1 Biozentrum [Basel, Suisse]
2 SIB - Swiss Institute of Bioinformatics [Genève]
3 Genome Center [UC Davis]
4 EPFL - Ecole Polytechnique Fédérale de Lausanne
5 UNIMI - Università degli Studi di Milano = University of Milan
6 NYU Grossman School of Medicine - New York University School of Medicine
7 IBS - UMR 5075 - Institut de biologie structurale
8 University of Birmingham [Birmingham]
9 MIT - Massachusetts Institute of Technology
10 Edin. - University of Edinburgh
11 Department of Chemistry [Ann Arbor]
12 Universität Bielefeld = Bielefeld University
13 University of Otago [Dunedin, Nouvelle-Zélande]
14 The Wellcome Trust Centre for Human Genetics [Oxford]
15 Monash University [Clayton]
16 Max Planck Institute for Developmental Biology
17 LISCB - Leicester Institute of Structural and Chemical Biology [Leicester]
18 University of Oxford
19 Department of Biology and Biocenter Oulu
20 UiB - University of Bergen
21 UCLA - University of California [Los Angeles]
22 Lanzhou University
23 Rice University [Houston]
24 [Northwestern University Medical School] - Feinberg School of Medicine [Northwestern University, Evanston]
25 Georg-August-University = Georg-August-Universität Göttingen
26 Institute of Agricultural Biology and Biotechnology
27 University of Nebraska–Lincoln
28 UC Davis - University of California [Davis]
29 UKE - Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg]
30 LIV - Leibniz-Institut für Virologie [Hamburg]
31 IBBR - Institute for Bioscience and Biotechnology Research [Rockville, MD, États-Unis]
Leila T. Alexander
Biozentrum [Basel, Suisse]
Swiss Institute of Bioinformatics [Genève]
Janani Durairaj
Biozentrum [Basel, Suisse]
Swiss Institute of Bioinformatics [Genève]
Andriy Kryshtafovych
Genome Center [UC Davis]
Luciano A. Abriata
Ecole Polytechnique Fédérale de Lausanne
Yusupha Bayo
  • Fonction : Auteur
Università degli Studi di Milano = University of Milan
Gira Bhabha
New York University School of Medicine
Cécile Breyton
Institut de biologie structurale
Simon Caulton
University of Birmingham [Birmingham]
James Chen
Massachusetts Institute of Technology
Séraphine Degroux
Institut de biologie structurale
Damian Ekiert
New York University School of Medicine
Benedikte Erlandsen
University of Edinburgh
Peter Freddolino
Department of Chemistry [Ann Arbor]
Dominic Gilzer
Universität Bielefeld = Bielefeld University
Chris Greening
University of Otago [Dunedin, Nouvelle-Zélande]
Jonathan Grimes
The Wellcome Trust Centre for Human Genetics [Oxford]
Rhys Grinter
Monash University [Clayton]
Manickam Gurusaran
University of Edinburgh
Marcus Hartmann
Max Planck Institute for Developmental Biology
Charlie Hitchman
  • Fonction : Auteur
Leicester Institute of Structural and Chemical Biology [Leicester]
Jeremy Keown
University of Oxford
Ashleigh Kropp
Monash University [Clayton]
Petri Kursula
Department of Biology and Biocenter Oulu
University of Bergen
Andrew Lovering
University of Birmingham [Birmingham]
Bruno Lemaitre
Ecole Polytechnique Fédérale de Lausanne
Andrea Lia
Leicester Institute of Structural and Chemical Biology [Leicester]
Shiheng Liu
University of California [Los Angeles]
Maria Logotheti
Max Planck Institute for Developmental Biology
Shuze Lu
  • Fonction : Auteur
Lanzhou University
Sigurbjörn Markússon
University of Bergen
Mitchell Miller
Rice University [Houston]
George Minasov
Feinberg School of Medicine [Northwestern University, Evanston]
Hartmut Niemann
Universität Bielefeld = Bielefeld University
Felipe Opazo
Georg-August-University = Georg-August-Universität Göttingen
George Phillips
Rice University [Houston]
Owen R. Davies
University of Edinburgh
Samuel Rommelaere
Ecole Polytechnique Fédérale de Lausanne
Monica Rosas-Lemus
Feinberg School of Medicine [Northwestern University, Evanston]
Pietro Roversi
Institute of Agricultural Biology and Biotechnology
Karla Satchell
Feinberg School of Medicine [Northwestern University, Evanston]
Nathan Smith
  • Fonction : Auteur
University of Nebraska–Lincoln
Mark Wilson
University of Nebraska–Lincoln
Kuan-Lin Wu
  • Fonction : Auteur
Rice University [Houston]
Xian Xia
University of California [Los Angeles]
Han Xiao
Rice University [Houston]
Wenhua Zhang
Lanzhou University
Z. Hong Zhou
  • Fonction : Auteur
University of California [Los Angeles]
Krzysztof Fidelis
University of California [Davis]
Maya Topf
Universitaetsklinikum Hamburg-Eppendorf = University Medical Center Hamburg-Eppendorf [Hamburg]
Leibniz-Institut für Virologie [Hamburg]
John Moult
Institute for Bioscience and Biotechnology Research [Rockville, MD, États-Unis]
Torsten Schwede
Biozentrum [Basel, Suisse]

Résumé

We 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.

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https://hal.science/hal-04231019

Soumis le : mercredi 22 novembre 2023-14:15:25

Dernière modification le : jeudi 10 octobre 2024-09:40:29

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hal-04231019 , version 1 (22-11-2023)

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Leila T. Alexander, Janani Durairaj, Andriy Kryshtafovych, Luciano A. Abriata, Yusupha Bayo, et al.. Protein target highlights in CASP15 : Analysis of models by structure providers. Proteins - Structure, Function and Bioinformatics, 2023, 2023, prot.26545. ⟨10.1002/prot.26545⟩. ⟨hal-04231019⟩

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