Assessment of chemical-crosslink-assisted protein structure modeling in CASP13
| العنوان: | Assessment of chemical-crosslink-assisted protein structure modeling in CASP13 |
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| المؤلفون: | Bohdan Monastyrskyy, Juri Rappsilber, Krzysztof Fidelis, J. Eduardo Fajardo, Mikhail Karasikov, Alexander Leitner, Agnieszka S. Karczyńska, Andras Fiser, Adam Belsom, Silvia Crivelli, Emilia A. Lubecka, Celina Sikorska, Andriy Kryshtafovych, Nelson Gil, Cezary Czaplewski, Rojan Shrestha, Esben Trabjerg, Sergei Grudinin, Guillaume Pagès, Adam Liwo, Adam K. Sieradzan |
| المساهمون: | Department of Systems & Computational Biology [New York], Albert Einstein College of Medicine [New York], Department of Biochemistry [New York], Institut für Biotechnologie [berlin], Technische Universität Berlin (TU), Department of Computer Science [Davis] (UC Davis), University of California [Davis] (UC Davis), University of California-University of California, Department of Environmental Analytics [Univ Gdańsk], Faculty of Chemistry [Univ Gdańsk], University of Gdańsk (UG)-University of Gdańsk (UG), Genome Center [UC Davis], Algorithms for Modeling and Simulation of Nanosystems (NANO-D), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Laboratoire Jean Kuntzmann (LJK ), Institut polytechnique de Grenoble - Grenoble Institute of Technology (Grenoble INP )-Institut National de Recherche en Informatique et en Automatique (Inria)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Moscow Institute of Physics and Technology [Moscow] (MIPT), Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Department of Computer Science [ETH Zürich] (D-INFK), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institute of Molecular Systems Biology [Zurich], Korea Institute for Advanced Study (KIAS), Institute of Mathematics [Univ Gdańsk], University of Gdańsk (UG), Wellcome Trust Centre for Cell Biology, University of Edinburgh, Technical University of Berlin / Technische Universität Berlin (TU), Department of Computer Science [Univ California Davis] (CS - UC Davis), University of California (UC)-University of California (UC), Algorithms for Modeling and Simulating Nanosystems [2018-...] (NANO-D-POST [2018-2020]), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria) |
| المصدر: | Proteins-Structure, Function and Bioinformatics Proteins-Structure, Function and Bioinformatics, Wiley, 2019, Critical Assessment of Methods of Protein Structure Prediction (CASP) Special Issue, 87 (12), pp.1283-1297. ⟨10.1002/prot.25816⟩ Proteins Proteins-Structure, Function and Bioinformatics, 2019, Critical Assessment of Methods of Protein Structure Prediction (CASP) Special Issue, 87 (12), pp.1283-1297. ⟨10.1002/prot.25816⟩ 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, 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 |
| سنة النشر: | 2019 |
| مصطلحات موضوعية: | CASP13, Models, Molecular, Computer science, Protein Conformation, Context (language use), Computational biology, Routine practice, 010402 general chemistry, Mass spectrometry, Machine learning, computer.software_genre, 01 natural sciences, Biochemistry, Article, [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph], 03 medical and health sciences, Protein structure, chemical-crosslink-assisted protein structure modeling, Structural Biology, Tandem Mass Spectrometry, Molecular Biology, 030304 developmental biology, 0303 health sciences, Chemistry, business.industry, 030302 biochemistry & molecular biology, Model protein, Computational Biology, Proteins, Reproducibility of Results, 0104 chemical sciences, [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics, Workflow, Cross-Linking Reagents, Models, Chemical, chemical crosslinking/mass spectrometry, Critical assessment, Artificial intelligence, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Protein structure modeling, computer, Function (biology), Algorithms, Chromatography, Liquid |
| الوصف: | International audience; 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. |
| وصف الملف: | application/pdf |
| تدمد: | 1097-0134 0887-3585 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::3892ed07b6cd880b9e30c43694e4aed5 https://pubmed.ncbi.nlm.nih.gov/31977133 |
| حقوق: | OPEN |
| رقم الأكسشن: | edsair.doi.dedup.....3892ed07b6cd880b9e30c43694e4aed5 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 10970134 08873585 |
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