title: Performance of the WeNMR CS-Rosetta3 web server in CASD-NMR.
abstract: We present here the performance of the WeNMR CS-Rosetta3 web server in CASD-NMR, the critical assessment of automated structure determination by NMR. The CS-Rosetta server uses only chemical shifts for structure prediction, in combination, when available, with a post-scoring procedure based on unassigned NOE lists (Huang et al. in J Am Chem Soc 127:1665-1674, 2005b, doi: 10.1021/ja047109h). We compare the original submissions using a previous version of the server based on Rosetta version 2.6 with recalculated targets using the new R3FP fragment picker for fragment selection and implementing a new annotation of prediction reliability (van der Schot et al. in J Biomol NMR 57:27-35, 2013, doi: 10.1007/s10858-013-9762-6), both implemented in the CS-Rosetta3 WeNMR server. In this second round of CASD-NMR, the WeNMR CS-Rosetta server has demonstrated a much better performance than in the first round since only converged targets were submitted. Further, recalculation of all CASD-NMR targets using the new version of the server demonstrates that our new annotation of prediction quality is giving reliable results. Predictions annotated as weak are often found to provide useful models, but only for a fraction of the sequence, and should therefore only be used with caution.
authors.affiliation: Faculty of Science - Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.|Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, 75 124, Uppsala, Sweden.
authors.forename: Gijs
authors.initials: G
authors.lastname: van der Schot
authors.affiliation: Faculty of Science - Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands. a.m.j.j.bonvin@uu.nl.
authors.forename: Alexandre M J J
authors.identifier: http://orcid.org/0000-0001-7369-1322
authors.initials: AM
authors.lastname: Bonvin
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software; D064878:Web Browser
chemical_list: D011506:Proteins
keywords: Automated structure determination; Chemical shifts; Grid computing; NOE-based scoring