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 Trabjerg; Andras Fiser

doi:10.1002/prot.25816

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

Systems & Computational Biology

Research output: Contribution to journal › Article › peer-review

23 Scopus citations

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 language	English (US)
Pages (from-to)	1283-1297
Number of pages	15
Journal	Proteins: Structure, Function and Bioinformatics
Volume	87
Issue number	12
DOIs	https://doi.org/10.1002/prot.25816
State	Published - Dec 1 2019

Keywords

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

ASJC Scopus subject areas

Structural Biology
Biochemistry
Molecular Biology

Access to Document

10.1002/prot.25816

Cite this

Fajardo, J. E., Shrestha, R., Gil, N., Belsom, A., Crivelli, S. N., Czaplewski, C., Fidelis, K., Grudinin, S., Karasikov, M., Karczyńska, A. S., Kryshtafovych, A., Leitner, A., Liwo, A., Lubecka, E. A., Monastyrskyy, B., Pagès, G., Rappsilber, J., Sieradzan, A. K., Sikorska, C., ... Fiser, A. (2019). Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins: Structure, Function and Bioinformatics, 87(12), 1283-1297. https://doi.org/10.1002/prot.25816

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, vol. 87, no. 12, pp. 1283-1297. https://doi.org/10.1002/prot.25816

@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 = "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",

}

TY - JOUR

T1 - Assessment of chemical-crosslink-assisted protein structure modeling in CASP13

AU - Fajardo, J. Eduardo

AU - Shrestha, Rojan

AU - Gil, Nelson

AU - Belsom, Adam

AU - Crivelli, Silvia N.

AU - Czaplewski, Cezary

AU - Fidelis, Krzysztof

AU - Grudinin, Sergei

AU - Karasikov, Mikhail

AU - Karczyńska, Agnieszka S.

AU - Kryshtafovych, Andriy

AU - Leitner, Alexander

AU - Liwo, Adam

AU - Lubecka, Emilia A.

AU - Monastyrskyy, Bohdan

AU - Pagès, Guillaume

AU - Rappsilber, Juri

AU - Sieradzan, Adam K.

AU - Sikorska, Celina

AU - Trabjerg, Esben

AU - Fiser, Andras

PY - 2019/12/1

Y1 - 2019/12/1

N2 - 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.

AB - 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.

KW - CASP13

KW - chemical crosslinking/mass spectrometry

KW - chemical-crosslink-assisted protein structure modeling

UR - http://www.scopus.com/inward/record.url?scp=85073985095&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85073985095&partnerID=8YFLogxK

U2 - 10.1002/prot.25816

DO - 10.1002/prot.25816

M3 - Article

C2 - 31569265

AN - SCOPUS:85073985095

SN - 0887-3585

VL - 87

SP - 1283

EP - 1297

JO - Proteins: Structure, Function and Bioinformatics

JF - Proteins: Structure, Function and Bioinformatics

IS - 12

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this