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

Research output: Contribution to journal › Journal article › Research › peer-review

Standard

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, Vol. 87, No. 12, 01.12.2019, p. 1283-1297.

Research output: Contribution to journal › Journal article › Research › peer-review

Harvard

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

APA

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

Vancouver

Fajardo JE, Shrestha R, Gil N, Belsom A, Crivelli SN, Czaplewski C et al. Assessment of chemical-crosslink-assisted protein structure modeling in CASP13. Proteins: Structure, Function and Bioinformatics. 2019 Dec 1;87(12):1283-1297. https://doi.org/10.1002/prot.25816

Author

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 ; Vol. 87, No. 12. pp. 1283-1297.

Bibtex

@article{0a2c4786685c40cbad1efdb9e6d0f129,
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 = "Erratum: This article corrects the following: J. Eduardo Fajardo Rojan Shrestha Nelson Gil Adam Belsom Silvia N. Crivelli Cezary Czaplewski Krzysztof Fidelis Sergei Grudinin Mikhail Karasikov Agnieszka S. Karczy{\'n}ska … See all authors First published:03 January 2020 https://doi.org/10.1002/prot.25867",
year = "2019",
month = dec,
day = "1",
doi = "10.1002/prot.25816",
language = "English",
volume = "87",
pages = "1283--1297",
journal = "Proteins: Structure, Function, and Bioinformatics",
issn = "0887-3585",
publisher = "JohnWiley & Sons, Inc.",
number = "12",

}

RIS

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

N1 - Erratum: This article corrects the following: J. Eduardo Fajardo Rojan Shrestha Nelson Gil Adam Belsom Silvia N. Crivelli Cezary Czaplewski Krzysztof Fidelis Sergei Grudinin Mikhail Karasikov Agnieszka S. Karczyńska … See all authors First published:03 January 2020 https://doi.org/10.1002/prot.25867

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

U2 - 10.1002/prot.25816

DO - 10.1002/prot.25816

M3 - Journal article

C2 - 31569265

AN - SCOPUS:85073985095

VL - 87

SP - 1283

EP - 1297

JO - Proteins: Structure, Function, and Bioinformatics

JF - Proteins: Structure, Function, and Bioinformatics

SN - 0887-3585

IS - 12

ER -

ID: 238963690