Open AccessBeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy
Author(s) -
András Micsonai,
Éva Moussong,
Frank Wien,
Eszter Boros,
Henrietta Vadászi,
Nikoletta Murvai,
Young-Ho Lee,
Tamás Molnár,
Matthieu Réfrégiers,
Yuji Goto,
Ágnes Tantos,
József Kardos
Publication year - 2022
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkac345
Subject(s) - protein secondary structure , web server , in silico , biology , antiparallel (mathematics) , circular dichroism , computational biology , protein data bank (rcsb pdb) , protein structure , upload , homology modeling , crystallography , biological system , computer science , bioinformatics , genetics , physics , biochemistry , chemistry , world wide web , gene , the internet , quantum mechanics , magnetic field , enzyme
Circular dichroism (CD) spectroscopy is widely used to characterize the secondary structure composition of proteins. To derive accurate and detailed structural information from the CD spectra, we have developed the Beta Structure Selection (BeStSel) method (PNAS, 112, E3095), which can handle the spectral diversity of β-structured proteins. The BeStSel webserver provides this method with useful accessories to the community with the main goal to analyze single or multiple protein 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 method in accuracy and information content, moreover, it is capable of predicting the protein fold down to the topology/homology level of the CATH classification. A new module of the webserver helps to distinguish intrinsically disordered proteins by their CD spectrum. Secondary structure calculation for uploaded PDB files will help the experimental verification of protein MD and in silico modelling using CD spectroscopy. The server also calculates extinction coefficients from the primary sequence for CD users to determine the accurate protein concentrations which is a prerequisite for reliable secondary structure determination. The BeStSel server can be freely accessed at https://bestsel.elte.hu.