FragFit

FragFit models missing protein segments such as loops and hinge regions into cryo-electron microscopy (cryo-EM) density maps to enable accurate reconstruction of three-dimensional molecular structures.

Key Features:

• Segment modeling: Models protein segments ranging from 3 to 35 amino acids into cryo-EM density maps.
• Targeted regions: Addresses missing segments including loops and hinge regions in protein complexes.
• Fragment database: Utilizes a database of approximately 1 billion fragments derived from Protein Data Bank (PDB) structures that is regularly updated.
• Selection criteria: Selects fragments based on geometric compatibility, sequence similarity, and fit within the cryo-EM density map.

Scientific Applications:

• Completing cryo-EM models: Integrates missing segments to improve completeness and accuracy of cryo-EM-derived structural models.
• Resolving flexible regions: Provides candidate conformations for loops and hinge regions that are poorly resolved by conventional methods.
• Structural interpretation: Aids interpretation of three-dimensional arrangements in molecular complexes from cryo-EM data.

Methodology:

Searches a PDB-derived fragment database (~1 billion entries) for fragments of matching length (3–35 amino acids) and sequence similarity, filters candidates by geometric compatibility, and evaluates their fit within the cryo-EM density map to select fragments for modeling.