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

Leila T. Alexander; Janani Durairaj; Andriy Kryshtafovych; Luciano A. Abriata; Yusupha Bayo; Gira Bhabha; Cécile Breyton; Simon G. Caulton; James Chen; Séraphine Degroux; Damian C. Ekiert; Benedikte S. Erlandsen; Peter L. Freddolino; Dominic Gilzer; Chris Greening; Jonathan M. Grimes; Rhys Grinter; Manickam Gurusaran; Marcus D. Hartmann; Charlie J. Hitchman; Jeremy R. Keown; Ashleigh Kropp; Petri Kursula; Andrew L. Lovering; Bruno Lemaitre; Andrea Lia; Shiheng Liu; Maria Logotheti; Shuze Lu; Sigurbjörn Markússon; Mitchell D. Miller; George Minasov; Hartmut H. Niemann; Felipe Opazo; George N. Phillips; Owen R. Davies; Samuel Rommelaere; Monica Rosas‐Lemus; Pietro Roversi; Karla Satchell; Nathan Smith; Mark A. Wilson; Kuan‐Lin Wu; Xian Xia; Han Xiao; Wenhua Zhang; Z. Hong Zhou; Krzysztof Fidelis; Maya Topf; John Moult; Torsten Schwede

doi:10.1002/prot.26545

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

Leila T. Alexander^*, Janani Durairaj, Andriy Kryshtafovych, Luciano A. Abriata, Yusupha Bayo, Gira Bhabha, Cécile Breyton, Simon G. Caulton, James Chen, Séraphine Degroux, Damian C. Ekiert, Benedikte S. Erlandsen, Peter L. Freddolino, Dominic Gilzer, Chris Greening, Jonathan M. Grimes, Rhys Grinter, Manickam Gurusaran, Marcus D. Hartmann, Charlie J. HitchmanJeremy R. Keown, Ashleigh Kropp, Petri Kursula, Andrew L. Lovering, Bruno Lemaitre, Andrea Lia, Shiheng Liu, Maria Logotheti, Shuze Lu, Sigurbjörn Markússon, Mitchell D. Miller, George Minasov, Hartmut H. Niemann, Felipe Opazo, George N. Phillips, Owen R. Davies, Samuel Rommelaere, Monica Rosas‐Lemus, Pietro Roversi, Karla Satchell, Nathan Smith, Mark A. Wilson, Kuan‐Lin Wu, Xian Xia, Han Xiao, Wenhua Zhang, Z. Hong Zhou, Krzysztof Fidelis, Maya Topf, John Moult, Torsten Schwede

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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Abstract

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.

Original language	English
Number of pages	29
Journal	Proteins: structure, function, and bioinformatics
Early online date	26 Jul 2023
DOIs	https://doi.org/10.1002/prot.26545
Publication status	E-pub ahead of print - 26 Jul 2023

Keywords

protein structure prediction
X‐ray crystallography
cryo‐EM
CASP

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Alexander, L. T., Durairaj, J., Kryshtafovych, A., Abriata, L. A., Bayo, Y., Bhabha, G., Breyton, C., Caulton, S. G., Chen, J., Degroux, S., Ekiert, D. C., Erlandsen, B. S., Freddolino, P. L., Gilzer, D., Greening, C., Grimes, J. M., Grinter, R., Gurusaran, M., Hartmann, M. D., ... Schwede, T. (2023). Protein target highlights in CASP15: Analysis of models by structure providers. Proteins: structure, function, and bioinformatics. Advance online publication. https://doi.org/10.1002/prot.26545

@article{fbc84adafe7c439d8e7cbc568ce5932b,

title = "Protein target highlights in CASP15: Analysis of models by structure providers",

abstract = "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.",

keywords = "protein structure prediction, X‐ray crystallography, cryo‐EM, CASP",

author = "Alexander, {Leila T.} and Janani Durairaj and Andriy Kryshtafovych and Abriata, {Luciano A.} and Yusupha Bayo and Gira Bhabha and C{\'e}cile Breyton and Caulton, {Simon G.} and James Chen and S{\'e}raphine Degroux and Ekiert, {Damian C.} and Erlandsen, {Benedikte S.} and Freddolino, {Peter L.} and Dominic Gilzer and Chris Greening and Grimes, {Jonathan M.} and Rhys Grinter and Manickam Gurusaran and Hartmann, {Marcus D.} and Hitchman, {Charlie J.} and Keown, {Jeremy R.} and Ashleigh Kropp and Petri Kursula and Lovering, {Andrew L.} and Bruno Lemaitre and Andrea Lia and Shiheng Liu and Maria Logotheti and Shuze Lu and Sigurbj{\"o}rn Mark{\'u}sson and Miller, {Mitchell D.} and George Minasov and Niemann, {Hartmut H.} and Felipe Opazo and Phillips, {George N.} and Davies, {Owen R.} and Samuel Rommelaere and Monica Rosas‐Lemus and Pietro Roversi and Karla Satchell and Nathan Smith and Wilson, {Mark A.} and Kuan‐Lin Wu and Xian Xia and Han Xiao and Wenhua Zhang and Zhou, {Z. Hong} and Krzysztof Fidelis and Maya Topf and John Moult and Torsten Schwede",

year = "2023",

month = jul,

day = "26",

doi = "10.1002/prot.26545",

language = "English",

journal = "Proteins: structure, function, and bioinformatics",

issn = "0887-3585",

publisher = "Wiley",

}

Alexander, LT, Durairaj, J, Kryshtafovych, A, Abriata, LA, Bayo, Y, Bhabha, G, Breyton, C, Caulton, SG, Chen, J, Degroux, S, Ekiert, DC, Erlandsen, BS, Freddolino, PL, Gilzer, D, Greening, C, Grimes, JM, Grinter, R, Gurusaran, M, Hartmann, MD, Hitchman, CJ, Keown, JR, Kropp, A, Kursula, P, Lovering, AL, Lemaitre, B, Lia, A, Liu, S, Logotheti, M, Lu, S, Markússon, S, Miller, MD, Minasov, G, Niemann, HH, Opazo, F, Phillips, GN, Davies, OR, Rommelaere, S, Rosas‐Lemus, M, Roversi, P, Satchell, K, Smith, N, Wilson, MA, Wu, KL, Xia, X, Xiao, H, Zhang, W, Zhou, ZH, Fidelis, K, Topf, M, Moult, J & Schwede, T 2023, 'Protein target highlights in CASP15: Analysis of models by structure providers', Proteins: structure, function, and bioinformatics. https://doi.org/10.1002/prot.26545

TY - JOUR

T1 - Protein target highlights in CASP15: Analysis of models by structure providers

AU - Alexander, Leila T.

AU - Durairaj, Janani

AU - Kryshtafovych, Andriy

AU - Abriata, Luciano A.

AU - Bayo, Yusupha

AU - Bhabha, Gira

AU - Breyton, Cécile

AU - Caulton, Simon G.

AU - Chen, James

AU - Degroux, Séraphine

AU - Ekiert, Damian C.

AU - Erlandsen, Benedikte S.

AU - Freddolino, Peter L.

AU - Gilzer, Dominic

AU - Greening, Chris

AU - Grimes, Jonathan M.

AU - Grinter, Rhys

AU - Gurusaran, Manickam

AU - Hartmann, Marcus D.

AU - Hitchman, Charlie J.

AU - Keown, Jeremy R.

AU - Kropp, Ashleigh

AU - Kursula, Petri

AU - Lovering, Andrew L.

AU - Lemaitre, Bruno

AU - Lia, Andrea

AU - Liu, Shiheng

AU - Logotheti, Maria

AU - Lu, Shuze

AU - Markússon, Sigurbjörn

AU - Miller, Mitchell D.

AU - Minasov, George

AU - Niemann, Hartmut H.

AU - Opazo, Felipe

AU - Phillips, George N.

AU - Davies, Owen R.

AU - Rommelaere, Samuel

AU - Rosas‐Lemus, Monica

AU - Roversi, Pietro

AU - Satchell, Karla

AU - Smith, Nathan

AU - Wilson, Mark A.

AU - Wu, Kuan‐Lin

AU - Xia, Xian

AU - Xiao, Han

AU - Zhang, Wenhua

AU - Zhou, Z. Hong

AU - Fidelis, Krzysztof

AU - Topf, Maya

AU - Moult, John

AU - Schwede, Torsten

PY - 2023/7/26

Y1 - 2023/7/26

N2 - 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.

AB - 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.

KW - protein structure prediction

KW - X‐ray crystallography

KW - cryo‐EM

KW - CASP

U2 - 10.1002/prot.26545

DO - 10.1002/prot.26545

M3 - Article

SN - 0887-3585

JO - Proteins: structure, function, and bioinformatics

JF - Proteins: structure, function, and bioinformatics

ER -

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

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Keywords

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