BeStSel

BeStSel analyzes protein secondary structure from circular dichroism (CD) spectroscopy, accounting for β-sheet orientation and twist to improve β-sheet content estimation and to predict protein fold topology within the CATH classification.

Key Features:

• Detailed secondary-structure decomposition: Identifies eight distinct secondary-structure components, including parallel-β structures and antiparallel β-sheets categorized into three groups based on twist.
• β-sheet orientation and twist modeling: Incorporates β-sheet orientation and twisting into the analysis algorithms to address CD spectral diversity of β-structures.
• Fold prediction: Predicts protein fold at the topology/homology level within the CATH protein fold classification system.
• CD data format and source support: Accepts normalized and raw CD spectra as single or multiple spectra and supports data from conventional CD equipment and synchrotron radiation sources.
• PDB structure integration and comparison: Analyzes Protein Data Bank (PDB) structures and compares BeStSel-derived secondary-structure contents with Dictionary of Secondary Structure of Proteins data.

Scientific Applications:

• Protein structure characterization: Provides precise estimates of β-sheet content and other secondary structures for proteins with complex folding patterns.
• Evolutionary studies: Uses fold prediction at the topology/homology level to assist analyses of evolutionary relationships among proteins.
• Functional analysis: Supplies detailed secondary-structure information to support investigations into protein function.

Methodology:

Algorithms deconvolve CD spectra while explicitly incorporating β-sheet orientation and twisting, and a module analyzes PDB structures and compares BeStSel-derived secondary-structure contents with the Dictionary of Secondary Structure of Proteins.