ScrewFit

ScrewFit analyzes protein structures to provide quantitative comparisons and geometrical descriptions of secondary structures and structural motifs relevant to ligand recognition.

Key Features:

• Quantitative Structure Comparison: Performs quantitative comparisons of protein conformations to detect subtle structural differences and similarities.
• Geometrical Modeling: Uses simple geometrical assumptions to model the spatial arrangement of amino acids and describe secondary-structure elements.
• Structural Motif Identification: Identifies and characterizes structural motifs relevant to protein function and ligand interactions.

Scientific Applications:

• Neuraminidase–oseltamivir analysis: Applied to study neuraminidase (NA) recognition by oseltamivir across subtypes including group-1 NA1, NA8 and group-2 NA9 and in influenza strains such as avian H5N1.
• Inhibitor design insights: Provides family-specific structural comparisons that inform the design of antiviral inhibitors by revealing subtype-dependent conformational effects.

Methodology:

Quantitatively compares protein structures to highlight ligand-induced conformational changes; models geometry of specific NA regions (Glu119; Arg130–Ser160; Val240–Gly260; Asp330–Glu382) to assess drug interactions; analyzes multiple conformations to derive conformational insights relevant to inhibitor design.