@article{0ff5639e1d5042ce8a8cd0759334267d,
title = "Assessment of chemical-crosslink-assisted protein structure modeling in CASP13",
abstract = "With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.",
keywords = "CASP13, chemical crosslinking/mass spectrometry, chemical-crosslink-assisted protein structure modeling",
author = "Fajardo, {J. Eduardo} and Rojan Shrestha and Nelson Gil and Adam Belsom and Crivelli, {Silvia N.} and Cezary Czaplewski and Krzysztof Fidelis and Sergei Grudinin and Mikhail Karasikov and Karczy{\'n}ska, {Agnieszka S.} and Andriy Kryshtafovych and Alexander Leitner and Adam Liwo and Lubecka, {Emilia A.} and Bohdan Monastyrskyy and Guillaume Pag{\`e}s and Juri Rappsilber and Sieradzan, {Adam K.} and Celina Sikorska and Esben Trabjerg and Andras Fiser",
note = "Funding Information: We thank Dr. I. Anishchanka and Dr. S. Ovchinnikov, University of Washington, for assistance in preparing contact‐distance restraints for group 492. This work was supported by the following grants and agencies: National Institutes of Health (NIH) grant GM118709, GM100482, and AI141816; L'Agence Nationale de la Recherche (grant number ANR‐15‐CE11‐0029‐03); National Science Center of Poland (Narodowe Centrum Nauki) (NCN), grants UMO‐2017/25/B/ST4/01026, UMO‐2017/26/M/ST4/00044, and UMO‐2017/27/B/ST4/00926; and the Benzon Foundation. Computational resources were provided by (a) the Interdisciplinary Centre of Mathematical and Computer Modeling (ICM) at the Uniwersytet Warszawski (b) the Centre of Informatics—Tricity Academic Supercomputer & networK (CI TASK) (c) the Polish Grid Infrastructure (PL‐GRID), and (d) our Beowulf cluster at the Faculty of Chemistry, University of Gda{\'n}sk. A.L. and E.T. would like to thank Ruedi Aebersold (ETH Zurich) for access to the Orbitrap Elite mass spectrometer and laboratory infrastructure. The CASP organizers and the Leitner and Rappsilber labs would also like to thank all groups that shared proteins and protein complexes for crosslinking experiments. Funding Information: We thank Dr. I. Anishchanka and Dr. S. Ovchinnikov, University of Washington, for assistance in preparing contact-distance restraints for group 492. This work was supported by the following grants and agencies: National Institutes of Health (NIH) grant GM118709, GM100482, and AI141816; L'Agence Nationale de la Recherche (grant number ANR-15-CE11-0029-03); National Science Center of Poland (Narodowe Centrum Nauki) (NCN), grants UMO-2017/25/B/ST4/01026, UMO-2017/26/M/ST4/00044, and UMO-2017/27/B/ST4/00926; and the Benzon Foundation. Computational resources were provided by (a) the Interdisciplinary Centre of Mathematical and Computer Modeling (ICM) at the Uniwersytet Warszawski (b) the Centre of Informatics?Tricity Academic Supercomputer & networK (CI TASK) (c) the Polish Grid Infrastructure (PL-GRID), and (d) our Beowulf cluster at the Faculty of Chemistry, University of Gda?sk. A.L. and E.T. would like to thank Ruedi Aebersold (ETH Zurich) for access to the Orbitrap Elite mass spectrometer and laboratory infrastructure. The CASP organizers and the Leitner and Rappsilber labs would also like to thank all groups that shared proteins and protein complexes for crosslinking experiments. Funding Information: Benzon Foundation; L'Agence Nationale de la Recherche, Grant/Award Number: ANR‐15‐CE11‐0029‐03; National Institute of Allergy and Infectious Diseases, Grant/Award Number: AI141816; National Institute of General Medical Sciences, Grant/Award Numbers: GM100482, GM118709; National Science Center of Poland, Grant/Award Numbers: UMO‐2017/25/B/ST4/01026, UMO‐2017/26/M/ST4/00044, UMO‐2017/27/B/ST4/00926 Funding information Publisher Copyright: {\textcopyright} 2019 Wiley Periodicals, Inc.",
year = "2019",
month = dec,
day = "1",
doi = "10.1002/prot.25816",
language = "English (US)",
volume = "87",
pages = "1283--1297",
journal = "Proteins: Structure, Function and Bioinformatics",
issn = "0887-3585",
publisher = "Wiley-Liss Inc.",
number = "12",
}