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

• DOI: 10.1002/prot.25816
• Publication Date: 2019-10-01T05:41:30Z
• Authors: J. Eduardo Fajardo; Rojan Shrestha; Nelson Gil; Adam Belsom; Silvia N. Crivelli; Cezary Czaplewski; Krzysztof Fidelis; Sergei Grudinin; Mikhail Karasikov; Agnieszka S. Karc...; Andriy Kryshtafovych; Alexander Leitner; Adam Liwo; Emilia A. Lubecka; Bohdan Monastyrskyy; Guillaume Pagès; Juri Rappsilber; Adam K. Sieradzan; Celina Sikorska; Esben Trabjerg; Andras Fiser
• Keywords: CASP13; Models, Molecular; 0301 basic medicine; 570; /dk/atira/pure/subjectarea/asjc/1300/1312; Bioinformatics; Protein Conformation; [PHYS.PHYS.PHYS-COMP-PH] Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph]; Bioinformatics and Computational Biology; 610; Mathematical sciences; [SDV.BBM.BP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biophysics; Chemical; Biochemistry; Mathematical Sciences; [PHYS.PHYS.PHYS-COMP-PH]Physics [physics]/Physics [physics]/Computational Physics [physics.comp-ph]; 03 medical and health sciences; Models; chemical-crosslink-assisted protein structure modeling; Structural Biology; Tandem Mass Spectrometry; Information and Computing Sciences; Molecular Biology; /dk/atira/pure/subjectarea/asjc/1300/1315; mass spectrometry; [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM]; Chromatography; Liquid; /dk/atira/pure/subjectarea/asjc/1300/1303; 0303 health sciences; Molecular; Computational Biology; Proteins; Reproducibility of Results; [SDV.BBM.BP]Life Sciences [q-bio]/Biochemistry; Biological Sciences; chemical crosslinking; Biological sciences; Cross-Linking Reagents; Models, Chemical; chemical crosslinking/mass spectrometry; Biochemistry and Cell Biology; [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]; Molecular Biology/Biophysics; Algorithms; chemical-crosslink-assisted protein structuremodeling; Chromatography, Liquid

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance accuracy protein structure modeling. Here, we review current state art in modeling structures with assistance experimentally determined within framework 13th meeting Critical Assessment Structure Prediction approaches. This largest-to-date blind assessment reveals benefits using data difficult to model prediction cases. However, broader context, it also suggests that unprecedented predict contacts recent years, will be useful only if their specificity further improved they are better integrated into computational workflows.