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Instruments / Technical Area	Publication Details	Published
	Outcomes of the EMDataResource cryo-EM ligand modeling challenge Catherine L. Lawson , Andriy Kryshtafovych , Grigore D. Pintilie , Stephen Burley , Jiří Černý , Vincent B. Chen , Paul Emsley , Alberto Gobbi , Andrzej Joachimiak , Sigrid Noreng , Michael G. Prisant , Randy J. Read , Jane S. Richardson , Alexis L. Rohou , Bohdan Schneider , Benjamin D. Sellers , Chenghua Shao , Elizabeth Sourial , Chris I. Williams , Christopher J. Williams , Ying Yang , Venkat Abbaraju , Pavel V. Afonine , Matthew L. Baker , Paul S. Bond , Tom L. Blundell , Tom Burnley , Arthur Campbell , Renzhi Cao , Jianlin Cheng , Grzegorz Chojnowski , Kevin D. Cowtan , Frank Dimaio , Reza Esmaeeli , Nabin Giri , Helmut Grubmüller , Soon Wen Hoh , Jie Hou , Corey F. Hryc , Carola Hunte , Maxim Igaev , Agnel P. Joseph , Wei-Chun Kao , Daisuke Kihara , Dilip Kumar , Lijun Lang , Sean Lin , Sai R. Maddhuri Venkata Subramaniya , Sumit Mittal , Arup Mondal , Nigel W. Moriarty , Andrew Muenks , Garib N. Murshudov , Robert A. Nicholls , Mateusz Olek , Colin M. Palmer , Alberto Perez , Emmi Pohjolainen , Karunakar R. Pothula , Christopher N. Rowley , Daipayan Sarkar , Luisa U. Schäfer , Christopher J. Schlicksup , Gunnar F. Schröder , Mrinal Shekhar , Dong Si , Abhishek Singharoy , Oleg V. Sobolev , Genki Terashi , Andrea C. Vaiana , Sundeep C. Vedithi , Jacob Verburgt , Xiao Wang , Rangana Warshamanage , Martyn Winn , Simone Weyand , Keitaro Yamashita , Minglei Zhao , Michael F. Schmid , Helen M. Berman , Wah Chiu Nature Methods 24 DOI: 10.1038/s41592-024-02321-7 Show Abstract ▼ Abstract: The EMDataResource Ligand Model Challenge aimed to assess the reliability and reproducibility of modeling ligands bound to protein and protein–nucleic acid complexes in cryogenic electron microscopy (cryo-EM) maps determined at near-atomic (1.9–2.5 Å) resolution. Three published maps were selected as targets: Escherichia coli beta-galactosidase with inhibitor, SARS-CoV-2 virus RNA-dependent RNA polymerase with covalently bound nucleotide analog and SARS-CoV-2 virus ion channel ORF3a with bound lipid. Sixty-one models were submitted from 17 independent research groups, each with supporting workflow details. The quality of submitted ligand models and surrounding atoms were analyzed by visual inspection and quantification of local map quality, model-to-map fit, geometry, energetics and contact scores. A composite rather than a single score was needed to assess macromolecule+ligand model quality. These observations lead us to recommend best practices for assessing cryo-EM structures of liganded macromolecules reported at near-atomic resolution.	Jun 2024
	Tertiary structure assessment at CASP15 Adam J. Simpkin , Shahram Mesdaghi , Filomeno Sanchez Rodriguez , Luc Elliott , David L. Murphy , Andriy Kryshtafovych , Ronan M. Keegan , Daniel J. Rigden Proteins: Structure, Function, And Bioinformatics 23 DOI: 10.1002/prot.26593 Open Access Show Abstract ▼ Abstract: The results of tertiary structure assessment at CASP15 are reported. For the first time, recognizing the outstanding performance of AlphaFold 2 (AF2) at CASP14, all single-chain predictions were assessed together, irrespective of whether a template was available. At CASP15, there was no single stand-out group, with most of the best-scoring groups—led by PEZYFoldings, UM-TBM, and Yang Server—employing AF2 in one way or another. Many top groups paid special attention to generating deep Multiple Sequence Alignments (MSAs) and testing variant MSAs, thereby allowing them to successfully address some of the hardest targets. Such difficult targets, as well as lacking templates, were typically proteins with few homologues. Local divergence between prediction and target correlated with localization at crystal lattice or chain interfaces, and with regions exhibiting high B-factor factors in crystal structure targets, and should not necessarily be considered as representing error in the prediction. However, analysis of exposed and buried side chain accuracy showed room for improvement even in the latter. Nevertheless, a majority of groups produced high-quality predictions for most targets, which are valuable for experimental structure determination, functional analysis, and many other tasks across biology. These include those applying methods similar to those used to generate major resources such as the AlphaFold Protein Structure Database and the ESM Metagenomic atlas: the confidence estimates of the former were also notably accurate.	Sep 2023
VMXm-Versatile Macromolecular Crystallography microfocus	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 , Sigurbjorn Markusson , 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 Proteins: Structure, Function, And Bioinformatics 78 DOI: 10.1002/prot.26545 Diamond Proposal Number(s): [19946, 23570, 27314, 28534] Open Access Show Abstract ▼ 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.	Jul 2023
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 Open Access 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
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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