ModFlex

ModFlex explores protein structural diversity to inform template selection for homology-based protein structure modeling.

Key Features:

• Integration with PDBFlex database: Leverages PDBFlex, which clusters protein structures extracted from the Protein Data Bank (PDB) based on sequence identity so each cluster represents a unique protein.
• Subcluster analysis for conformational diversity: Organizes structures within each cluster into subclusters based on structural similarity, with each subcluster representing a distinct conformation.
• Template selection informed by conformational and functional considerations: Provides analyses to support choosing templates that reflect relevant functional states and structural variability for homology modeling of proteins known only by their amino acid sequence.
• Integration with analytical programs for flexibility and divergence analysis: Interfaces with other programs and servers to analyze and visualize protein structural flexibility and divergence.
• Addressing gaps in homology modeling: Offers insights into conformational diversity when multiple structural templates are available to improve modeling decisions.

Scientific Applications:

• Protein function and dynamics: Supports studies of protein function, dynamics, and interactions by enabling consideration of multiple conformations relevant to different functional states.
• Homology modeling of uncharacterized proteins: Aids modeling of proteins known only by their amino acid sequence by facilitating selection among diverse structural templates.
• Structure–function hypothesis generation: Exposes conformational landscapes and structural variations to inform hypotheses about structure–function relationships.

Methodology:

Clusters protein structures from the Protein Data Bank (PDB) by sequence identity via PDBFlex, further groups structures into subclusters by structural similarity, and integrates with other programs and servers for analysis and visualization of structural flexibility and divergence.