Bestsel: Updated webserver for secondary structure and fold prediction for protein CD spectroscopy.

Abstract

Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure of proteins. Recently, we have developed the Beta Structure Selection (BeStSel) method to derive accurate and detailed structural information from the CD spectra which handles the spectral diversity of β-structured proteins. The BeStSel webserver provides a user-friendly and intelligent interface for the analysis of single or multiple CD spectra. Uniquely, BeStSel provides information on eight secondary structure components including parallel β-structure and antiparallel β-sheets with three different groups of twist. It overperforms any available methods in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. With the new versions of the DSSP and CATH databases, even more accurate estimates can be obtained using re-optimised basis spectra. A new module of the updated webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Users can also enter PDB IDs or upload structure files in PDB format as input to determine the corresponding secondary structure contents and fold classification, which help the experimental verification of protein MD and in silico modelling using CD spectroscopy. To aid correct concentration determination, extinction coefficients at 205 and 214 nm can be calculated from the primary sequence of the protein. The BeStSel server can be freely accessed at https://bestsel.elte.hu. This work was supported by National Research, Development and Innovation Fund of Hungary (K120391, KH125597, 2017-1.2.1-NKP-2017-00002, FIEK_16-1-2016-0005, TÉT_16-1-2016-0134, TÉT_16-1-2016-0197); SOLEIL Synchrotron, France (proposals 20171582, 20160916, 20151300, 20150515).