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Instruments / Technical Area	Publication Details	Published
I03-Macromolecular Crystallography	Target highlights in CASP14 : Analysis of models by structure providers Leila T. Alexander , Rosalba Lepore , Andriy Kryshtafovych , Athanasios Adamopoulos , Markus Alahuhta , Ann M. Arvin , Yannick J. Bomble , Bettina Böttcher , Cécile Breyton , Valerio Chiarini , Naga Babu Chinnam , Wah Chiu , Krzysztof Fidelis , Rhys Grinter , Gagan D. Gupta , Marcus D. Hartmann , Christopher S. Hayes , Tatjana Heidebrecht , Andrea Ilari , Andrzej Joachimiak , Youngchang Kim , Romain Linares , Andrew L. Lovering , Vladimir V. Lunin , Andrei N. Lupas , Cihan Makbul , Karolina Michalska , John Moult , Prasun K. Mukherjee , William Nutt , Stefan L. Oliver , Anastassis Perrakis , Lucy Stols , John A. Tainer , Maya Topf , Susan E. Tsutakawa , Mauricio Valdivia‐delgado , Torsten Schwede Proteins: Structure, Function, And Bioinformatics 89, 1647 - 1672 DOI: 10.1002/prot.26247 Open Access Show Abstract ▼ Abstract: The biological and functional significance of selected Critical Assessment of Techniques for Protein Structure Prediction 14 (CASP14) targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modeled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins.	Dec 2021
	Evaluation of model refinement in CASP14 Adam J. Simpkin , Filomeno Sanchez Rodriguez , Shahram Mesdaghi , Andriy Kryshtafovych , Daniel J. Rigden Proteins: Structure, Function, And Bioinformatics DOI: 10.1002/prot.26185 Show Abstract ▼ Abstract: We report here an assessment of the model refinement category of the 14th round of Critical Assessment of Structure Prediction (CASP14). As before, predictors submitted up to five ranked refinements, along with associated residue-level error estimates, for targets that had a wide range of starting quality. The ability of groups to accurately rank their submissions and to predict coordinate error varied widely. Overall only four groups out-performed a “naïve predictor” corresponding to resubmission of the starting model. Among the top groups there are interesting differences of approach and in the spread of improvements seen: some methods are more conservative, others more adventurous. Some targets were “double-barrelled” for which predictors were offered a high-quality AlphaFold 2 (AF2)-derived prediction alongside another of lower quality. The AF2-derived models were largely unimprovable, many of their apparent errors being found to reside at domain and, especially, crystal lattice contacts. Refinement is shown to have a mixed impact overall on structure-based function annotation methods to predict nucleic acid binding, spot catalytic sites and dock protein structures.	Jul 2021
I02-Macromolecular Crystallography I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I04-Macromolecular Crystallography	Target highlights in CASP13: Experimental target structures through the eyes of their authors Rosalba Lepore , Andriy Kryshtafovych , Markus Alahuhta , Harshul A. Veraszto , Yannick J. Bomble , Joshua C. Bufton , Alex N. Bullock , Cody Caba , Hongnan Cao , Owen R. Davies , Ambroise Desfosses , Matthew Dunne , Krzysztof Fidelis , Celia W. Goulding , Manickam Gurusaran , Irina Gutsche , Christopher J. Harding , Marcus D. Hartmann , Christopher S. Hayes , Andrzej Joachimiak , Petr G. Leiman , Peter Loppnau , Andrew L. Lovering , Vladimir V. Lunin , Karolina Michalska , Ignacio Mir‐sanchis , Alok Mitra , John Moult , George N. Phillips Jr , Daniel Pinkas , Phoebe A. Rice , Yufeng Tong , Maya Topf , Jonathan D. Walton , Torsten Schwede Proteins: Structure, Function, And Bioinformatics 7 DOI: 10.1002/prot.25805 Diamond Proposal Number(s): [14692] Open Access Show Abstract ▼ Abstract: The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.	Sep 2019
	Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016) Andriy Kryshtafovych , Reinhard Albrecht , Arnaud Basle , Pedro Bule , Alessandro T. Caputo , Ana Luisa Carvalho , Kinlin L. Chao , Ron Diskin , Krzysztof Fidelis , Carlos M. G. A. Fontes , Folmer Fredslund , Harry J. Gilbert , Celia W. Goulding , Marcus D. Hartmann , Christopher S. Hayes , Osnat Herzberg , Johan C. Hill , Andrzej Joachimiak , Gert-Wieland Kohring , Roman I. Koning , Leila Lo Leggio , Marco Mangiagalli , Karolina Michalska , John Moult , Shabir Najmudin , Marco Nardini , Valentina Nardone , Didier Ndeh , Thanh-Hong Nguyen , Guido Pintacuda , Sandra Postel , Mark J. Van Raaij , Pietro Roversi , Amir Shimon , Abhimanyu K. Singh , Eric J. Sundberg , Kaspars Tars , Nicole Zitzmann , Torsten Schwede Proteins: Structure, Function, And Bioinformatics 86, 27 - 50 DOI: 10.1002/prot.25392 Show Abstract ▼ Abstract: The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment.	Mar 2018
I03-Macromolecular Crystallography	Some of the most interesting CASP11 targets through the eyes of their authors Andriy Kryshtafovych , John Moult , Arnaud Basle , Alex Burgin , Timothy K. Craig , Robert A. Edwards , Deborah Fass , Marcus Hartmann , Mateusz Korycinski , Rick Lewis , Donald Lorimer , Andrei N. Lupas , Janet Newman , Thomas S. Peat , Kurt H. Piepenbrink , Janani Prahlad , Mark Van Raaij , Forest Rohwer , Anca M. Segall , Victor Seguritan , Eric J. Sundberg , Abhimanyu Singh , Mark A. Wilson , Torsten Schwede Proteins: Structure, Function, And Bioinformatics DOI: 10.1002/prot.24942 Diamond Proposal Number(s): [9948] Open Access Show Abstract ▼ Abstract: The Critical Assessment of protein Structure Prediction (CASP) experiment would not have been possible without the prediction targets provided by the experimental structural biology community. In this article, selected crystallographers providing targets for the CASP11 experiment discuss the functional and biological significance of the target proteins, highlight their most interesting structural features and assess whether these features were correctly reproduced in the predictions submitted to CASP11.	Oct 2015

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I03-Macromolecular Crystallography

Target highlights in CASP14 : Analysis of models by structure providers