Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

J. Eduardo Fajardo , Rojan Shrestha , Nelson Gil , Adam Belsom , Silvia N. Crivelli , Cezary Czaplewski , Krzysztof Fidelis , Sergei Grudinin , Mikhail Karasikov , Agnieszka Karczyńska , Andriy Kryshtafovych , Alexander Leitner , Józef Adam Liwo , Emilia Lubecka , Bohdan Monastyrskyy , Guillaume Pagès , Juri Rappsilber , Adam Sieradzan , Celina Sikorska , Esben Trabjerg , Andras Fiser

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.
Author J. Eduardo Fajardo
J. Eduardo Fajardo,,
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, Rojan Shrestha
Rojan Shrestha,,
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, Nelson Gil
Nelson Gil,,
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, Adam Belsom
Adam Belsom,,
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, Silvia N. Crivelli
Silvia N. Crivelli,,
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, Cezary Czaplewski (FCh / DTCh / LSP)
Cezary Czaplewski,,
- Laboratory of Simulation of Polymers
, Krzysztof Fidelis
Krzysztof Fidelis,,
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, Sergei Grudinin
Sergei Grudinin,,
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, Mikhail Karasikov
Mikhail Karasikov,,
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, Agnieszka Karczyńska (FCh / DTCh / LMM)
Agnieszka Karczyńska,,
- Laboratory of Molecular Modeling
et al.`
Journal seriesProteins-Structure Function and Bioinformatics, [Proteins: Structure, Function and Genetics], ISSN 0887-3585, e-ISSN 1097-0134, (N/A 100 pkt)
Issue year2019
Vol87
No12
Pages1283-1297
Publication size in sheets0.7
Keywords in EnglishCASP13, chemical crosslinking/mass spectrometry, chemical-crosslink-assisted protein structuremodeling
ASJC Classification1303 Biochemistry; 1312 Molecular Biology; 1315 Structural Biology
DOIDOI:10.1002/prot.25816
URL https://onlinelibrary.wiley.com/doi/epdf/10.1002/prot.25816
Languageen angielski
Score (nominal)100
Score sourcejournalList
ScoreMinisterial score = 100.0, 28-01-2020, ArticleFromJournal
Publication indicators WoS Citations = 2; Scopus SNIP (Source Normalised Impact per Paper): 2016 = 0.747; WoS Impact Factor: 2018 = 2.501 (2) - 2018=2.285 (5)
Citation count*6 (2020-03-27)
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* presented citation count is obtained through Internet information analysis and it is close to the number calculated by the Publish or Perish system.
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