FF - Fragment Finder

FF - Fragment Finder retrieves 3D protein structural fragments similar to user-defined motifs by comparing main chain backbone phi and psi angles against curated non-homologous protein-chain datasets for structural analysis and modeling.

Key Features:

• Input formats: Accepts a PDB ID, a structure coordinate file, or a list of phi and psi angles as query inputs.
• Curated datasets: Searches datasets composed of either 25% or 90% non-homologous protein chains to reduce sequence-homology bias.
• Backbone conformational comparison: Compares main chain backbone phi and psi angles between query motifs and dataset fragments to identify structural similarity.
• Motif superimposition: Performs structural superimposition of queried motifs and retrieved fragments to assess geometric similarity.

Scientific Applications:

• Protein design: Identifies structurally compatible fragments for incorporation into protein engineering and design workflows.
• Function prediction: Reveals structurally conserved motifs that can indicate potential functional sites independent of sequence similarity.
• Evolutionary analysis: Supports investigation of evolutionary relationships by highlighting conserved backbone conformations across non-homologous proteins.
• Conformational diversity exploration: Enables analysis of local backbone conformational variability within and between protein families.

Methodology:

Comparisons are performed by matching main chain backbone phi and psi angles of the input motif against entries in datasets of 25% or 90% non-homologous protein chains, followed by structural superimposition of matched fragments; the approach emphasizes angle-based comparison rather than sequence similarity.