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 S. Karczyńska, Andriy Kryshtafovych, Alexander Leitner, Adam Liwo, Emilia A. Lubecka, Bohdan Monastyrskyy, Guillaume Pagès, Juri Rappsilber, Adam K. Sieradzan, Celina Sikorska, Esben TrabjergAndras Fiser

Research output: Contribution to journalArticle

1 Citation (Scopus)

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.

Original languageEnglish (US)
JournalProteins: Structure, Function and Bioinformatics
DOIs
StateAccepted/In press - Jan 1 2019

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Proteins
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Crosslinking

Keywords

  • CASP13
  • chemical crosslinking/mass spectrometry
  • chemical-crosslink-assisted protein structure modeling

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Cite this

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. / Fajardo, J. Eduardo; Shrestha, Rojan; Gil, Nelson; Belsom, Adam; Crivelli, Silvia N.; Czaplewski, Cezary; Fidelis, Krzysztof; Grudinin, Sergei; Karasikov, Mikhail; Karczyńska, Agnieszka S.; Kryshtafovych, Andriy; Leitner, Alexander; Liwo, Adam; Lubecka, Emilia A.; Monastyrskyy, Bohdan; Pagès, Guillaume; Rappsilber, Juri; Sieradzan, Adam K.; Sikorska, Celina; Trabjerg, Esben; Fiser, Andras.

In: Proteins: Structure, Function and Bioinformatics, 01.01.2019.

Research output: Contribution to journalArticle

Fajardo, JE, Shrestha, R, Gil, N, Belsom, A, Crivelli, SN, Czaplewski, C, Fidelis, K, Grudinin, S, Karasikov, M, Karczyńska, AS, Kryshtafovych, A, Leitner, A, Liwo, A, Lubecka, EA, Monastyrskyy, B, Pagès, G, Rappsilber, J, Sieradzan, AK, Sikorska, C, Trabjerg, E & Fiser, A 2019, 'Assessment of chemical-crosslink-assisted protein structure modeling in CASP13', Proteins: Structure, Function and Bioinformatics. https://doi.org/10.1002/prot.25816
Fajardo, J. Eduardo ; Shrestha, Rojan ; Gil, Nelson ; Belsom, Adam ; Crivelli, Silvia N. ; Czaplewski, Cezary ; Fidelis, Krzysztof ; Grudinin, Sergei ; Karasikov, Mikhail ; Karczyńska, Agnieszka S. ; Kryshtafovych, Andriy ; Leitner, Alexander ; Liwo, Adam ; Lubecka, Emilia A. ; Monastyrskyy, Bohdan ; Pagès, Guillaume ; Rappsilber, Juri ; Sieradzan, Adam K. ; Sikorska, Celina ; Trabjerg, Esben ; Fiser, Andras. / Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. In: Proteins: Structure, Function and Bioinformatics. 2019.
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